Chakotay

Captain Chakotay was a 24th century Human male of Nicarao descent who served as a Starfleet officer before joining the Maquis. After his ship, the Val Jean, was transported and subsequently destroyed in the Delta Quadrant, he joined the crew of the starship as its first officer under Captain Kathryn Janeway during their seven-year journey back to Earth. () 
Following his stint on Voyager, Chakotay was promoted to Captain and given command of the . () The Protostar encountered a temporal anomaly that flung it into the 25th century and deposited it over Solum at a time when the native Vau N'Akat sought revenge on the Federation for catalyzing and not interfering in a catastrophic civil war. Chakotay was forced to send the Protostar back in time sans crew to prevent The Order from using a living construct to decimate the Federation, stranding him in an alternate future. Thanks to the efforts of the young crew who recovered the Protostar and , Starfleet received Chakotay's distress calls and Vice Admiral Janeway expressed an intention to find and rescue her old friend. ()
Following his successful rescue, Chakotay was given command of the . ()
== Early life and family ==
Chakotay was born in 2329 in the Federation colony on Trebus near the Cardassian Demilitarized Zone that his native tribe had moved to several generations earlier. Here, he was raised by his mother Tananka and his father, Kolopak, who considered him a "contrary" from the beginning because he had come out of his mother "upside down", as his father once remarked. (; ) 
Chakotay also had a sister and a cousin who lived in Ohio. () During an incident in 2373 that took Voyager to Earth in 1996, Chakotay considered "looking up" a few of his ancestors, noting that he knew of one ancestor at that time who worked as a school teacher in Arizona. () 
One of Chakotay's early ancestors was Ce Acatl, a man who was fathered by a white conqueror when they first took over Chakotay's tribe's native lands on Earth. ()
Being of Native American descent, Chakotay's tribe – mainly because of the intrusion of more technological societies – left Earth to find their own home on another planet near the Cardassian border. From an early age, his father tried to impart his values on Chakotay in many ways, such as taking him on hikes to nearby forested worlds of their ancestors. In 2344, he took Chakotay on a quest through the Central American rainforest, looking for their fellow descendants of the ancient Rubber Tree People that had never left the forest.
As a young man, Chakotay was rather resistant to his family's way of life and in a technologically advanced world often felt out of place among the members of his tribe who asserted a strong connection to their ancestral lands and spirits and lived a simple life. Chakotay dismissed his tribe that he believed lived in the past of fantasy and myth. He did not want to be part of that and instead wanted to be like all the other tribes that had embraced the 24th century. When his father would take him on expeditions to discover his roots and connection to the "sky spirits", Chakotay remained a reluctant participant, even ridiculing the sky spirits once by suggesting they had "taken a wrong turn" somewhere. () 
Chakotay also refused to hunt deer with his father. ()
Kolopak tried to teach Chakotay that without Spirits to guide him, he would lose his way. But Chakotay did not want to listen as he did not place much value in spirituality. He remained resistant, instead choosing to embrace technological advancement, believing that he was the master of his own life. One of Chakotay's childhood heroes was astronaut John Kelly. () 
While initially somewhat disappointed in his son's lack of interest in the culture and traditions of their tribe, Kolopak remained patient with Chakotay and, due to his son's curiosity, allowed him to read about other societies as he was growing up. He did so because he strongly believed that ignorance is one's greatest enemy. ()
However, by the time Chakotay was fifteen years old, he had already set his sights on Starfleet and greatly surprised his father when he told him that he was going to leave the tribe to attend Starfleet Academy. His father disapproved of his son's decision but was unable to convince him otherwise. ()
Chakotay and his father were not on good terms when Kolopak was killed while defending his colony against Cardassians. When the news reached Chakotay, he was unsure about how to reconcile their differences and heal their old wounds. To honor his father's memory and to continue the fight in his name, Chakotay resigned from Starfleet and joined the Maquis. It was then that he took the mark, the tattoo, on his forehead in order to honor the memory of his father and to signify his Native American heritage. () 
In the years following his resignation from Starfleet, he not only joined the Maquis to fight the Cardassians but he also finally began placing great faith in his spiritual background by taking pride in the stories and accomplishments of his people. He often embarked on vision quests to help guide his life and to commune with his father's spirit. He also used a medicine wheel to heal himself both spiritually and physically. ()
The Pakra was the name of the solitary ritual by which Chakotay commemorated the anniversary of Kolopak's death. On stardate 49005.3, Captain Janeway granted him the use of a shuttlecraft so he could perform the ritual in private. ()
When Chakotay was young, he looked after his grandfather, who suffered from hallucinations caused by an inherited defective gene. This gene was suppressed in Chakotay before birth, although it was activated for a brief period in 2375 by aliens who attempted to make contact with the crew of Voyager. ()
== Starfleet career ==
=== Starfleet Academy ===
At the age of fifteen, Chakotay entered Starfleet Academy, sponsored by Captain . Chakotay misled the officer into believing that he had Kolopak's permission to join. ()
Chakotay possessed great piloting skills and during his first year he trained as a pilot in North America. He then went to Venus for a couple of months to learn how to handle atmospheric storms and later dodged asteroids for a semester in the Sol system asteroid belt. ()
He also became a proficient boxer at the light heavyweight level, with a record of twenty-three wins and one loss. The loss was to a Nausicaan boxer with "a mean right hook." B'Elanna Torres once jested "legend has it that 'The Tattooed Terror' has put more men in sickbay than the Ankaran flu." () His personal trainer was Academy groundsman Boothby. ()
=== Starfleet officer ===
Chakotay graduated from Starfleet Academy in 2348. () 
On his first starship posting, he served during the planned first contact with the Tarkannans. After spending a lot of time pushing his captain to let him be on the diplomatic team, he began studying everything about them. When he finally came face to face with their delegation, he very proudly made the traditional gesture for "hello", not realizing that males and females have different styles of movement when making such symbolic gestures. He later found out that he had actually propositioned the ambassador. He remembered this encounter and mentioned it to Captain Janeway when in 2372 they made first contact with the Drayans, noting that it almost got his sent back to the Academy for remedial training. ()
On another assignment, he visited a tomb excavation on Ktaria VII on one of his earliest away missions. There, unaware of local custom, he – wanting to take a memento – stole a small stone from the burial. He was later informed that each stone represented a prayer and that he had desecrated the burial site. ()
On another occasion, he beamed down to a planet and the pattern buffer malfunctioned, misreading his Starfleet uniform. When he rematerialized, all he had was his combadge. ()
Once, while serving in Starfleet, he learned to communicate with a "Terrelian seapod"; something normally thought very difficult to communicate with. ()
== The Maquis ==
After his father was killed in 2368 while defending their colony, Chakotay resisted the Cardassian takeover of his planet – as per the terms of the border treaty between Cardassia and the Federation. He refused to stand by and watch his people be displaced once again, as had happened on Earth hundreds of years ago. () As such, he was one of the Maquis who were in the fight for principle, not mercenary gain or violent outlet. ()
On , 2368 he resigned from his position as an instructor in Starfleet's Advanced Tactical Training by submitting his resignation to Admiral Nimembeh. He was recruited in the Maquis by his old friend Sveta. ()
After joining the Maquis, he became one of its leaders and his one of the most successful in resisting the Cardassians and Federation. His vessel, the Val Jean, was his primary mode of space transportation. () Like captains of other ships, he would have conversation with his. () Aside from his Val Jean crew, including Seska, B'Elanna Torres, Ayala, and many others; Chakotay had other Maquis friends, including Li-Paz, Sahreen, Meyer and . ()
Among their various missions as Maquis, included an instance when Chakotay, Torres, and Seska successfully disabled the computer core on a Cardassian frigate, orbiting Bajor. This was accomplished when Seska modified an antiproton beam to penetrate the frigate's shields and hull from an extremely close range. ()
Around 2370, Chakotay encountered two Starfleet runabouts near Teluridian IV. Although outnumbered, the Val Jean was able to escape using the Maquis trick whereby they blew out the dorsal phase emitters and cut main power, making it look as if the ship was in serious trouble. ()
While trying to escape from a Cardassian warship commanded by Gul Evek in the Badlands, Chakotay and his crew, including Tuvok – Captain Janeway's security chief working undercover as a Maquis – were transported to the Delta Quadrant by the Caretaker's array. In an attempt to locate the disappeared Maquis ship, followed them into the Badlands, becoming trapped 70,000 light years away in the Delta Quadrant shortly after. ()
== Second Starfleet career ==
=== USS Voyager ===
After having made contact with Voyager and accepting the realization of being alone in an uncharted part of the galaxy, Chakotay agreed to cooperate with Janeway when both of their crews were abducted and subjected to medical testing by the . The crewmembers were eventually found, and the Caretaker's Array destroyed so it would not fall into the hands of the ruthless Kazon. 
In order to protect Voyager while it destroyed the Array, Chakotay crashed his ship into a Kazon carrier vessel.
Following the destruction of his ship in the Delta Quadrant, Chakotay and his crew joined Voyagers crew as one Starfleet crew in order to find a way home. He was granted the provisional rank of Commander and became Voyagers second in command. As first officer, he was in charge of all ship personnel and of protecting the captain, both roles which he threw himself into. A man of great moral conviction and courage, Chakotay embraced Starfleet principles once again and served Captain Janeway as first officer, forging a meaningful friendship with her; despite moments of strong disagreement, he was loyal to Janeway and the ship and helped keep the peace and establish cooperation and a positive rapport between the Maquis and the Starfleet crew. As the one responsible for the personnel, and as a friendly and approachable person, he was familiar with the crew and understood how they were feeling, more so than the captain. (, )
==== The first year (2371) ====
On appointment to First Officer, Chakotay was unsure if Janeway was using him as a "token" Maquis officer and confronts her about it while also advocating for his fellow Maquis members. However, his devotion to Voyager was strong, even though he never lost his sense of being Maquis: he even threatened to throw his Maquis crewmates Seska and Jarvin into the brig when they said they would support him in a mutiny against Janeway. When Tuvok wished to train a group of Maquis in order to bring them up to Starfleet standards, Chakotay forcefully persuaded them, after they initially resisted and wanted to do things "the Maquis way". ()
Chakotay was thrown into command of Voyager early on in his time as part of the crew when Janeway and Tom Paris become stuck a day in the past on a planet's surface. Chakotay had to command the ship and lead an away mission to find Janeway and Paris. In this command position, over the first few years Chakotay has a number of clashes with Tuvok, who had been spying on him in the Maquis and who would naturally have been Janeway's first officer under more usual circumstances. The two came to respect each other over the course of the years they serve together, however. ()
Despite his attempts to stay as neutral and objective as possible when it came to the merged crew, he sometimes felt the need to stand up for some of his former Maquis members, knowing that if he didn't stand up for them, no one else would. He, for example, recommended a hot-tempered B'Elanna Torres as chief engineer and was willing, against all odds, to give Seska the benefit of the doubt when she was accused of secretly collaborating with the enemy. () His recommendation of and advocacy for Torres was a vital moment for Voyager, not only helping to integrate the two crews, but also providing the ship with a truly brilliant engineer. While Janeway needed convincing, she quickly recognised the wisdom in Chakotay's work, telling him within their first two months in the Delta Quadrant, "A good choice for Chief Engineer, if I do say so myself". ()
He also had his share of personal disappointments after joining Voyager: he found out that Tuvok was a Federation spy and actually Captain Janeway's security chief sent to infiltrate his crew, Seska, his lover, was revealed to be a Cardassian spy who, now in the Delta Quadrant, had also begun to secretly collaborate with and transfer Federation technology to the Kazon, and he had to deal with Tom Paris, a person he not only disliked, but whom he actually considered to be nothing but a mercenary willing to sell out to the highest bidder. The betrayal of Seska was particularly hard on him, not only because he had an intimate relationship with her, but also because he had personally vouched for her. Her betrayal of his trust angered and humiliated Chakotay. When he confronted her, she told him that she did it for him and the crew because their captain was a fool and incapable of getting them home. Shortly after, Seska escaped from the ship and joined Maje Culluh of the Kazon Nistrim. ()
Chakotay's interests in anthropology and paleontology, and his respect for other cultures, is evident on a number of occasions during the voyage. They are revealed early on in the first year after an away mission uncovered that mineral deposits on an asteroid were part of decomposing remains in a burial site. Chakotay gathers a lot of information simply by observing closely, not wanting to show disrespect by even using passive tricorders scans. ()
Chakotay quickly and naturally fell into the role of informal spiritual guide and counsel to a number of the crew, including Janeway, who he guides on a vision quest to find her animal guide during their first months together. () In keeping with his character, this is understated role, something he is approached about or offers at appropriate times. ()
His tactical and piloting skills were also required from early on on Voyager. In one instance, with the usual helmsman unavailable, Chakotay used Maquis tactics to disable attacking ships. He stated, "out here in the Delta quadrant, every old trick is new again" and indicated he had many tricks to use. He also devised a way of detecting a hidden ship using Voyagers phasers. ()
During their first year in the Delta Quadrant, Voyager met a number of hostile species, including the Vidiians, who harvest organs from other species to perpetuate their own. The Vidiians were considered, along with the Borg and Species 8472, the prime examples of species hostile to Voyager in the Delta Quadrant. () During an ambush of Voyager within its first two months in the quadrant, Chakotay's Starfleet advanced tactical training combined with his Maquis ingenuity and tenacity saved the ship from being overwhelmed by the Vidiians, who had managed to attach a number of grapplers to Voyagers hull. Janeway absent from the bridge, Chakotay took charge and instructed Kim to reverse the hull's polarity in an effort to shake the grapplers off. Rerouting the deflector to discharge antigraviton pulses along the hull and engaging the inertial dampers started a controlled pitch of the ship and snapped a grappler off. Chakotay then ordered helm to reverse thrusters at full power, to resist the Vidiians deploying a tractor beam, despite objections from the crew that doing so could tear the hull apart. A section of the hull came away with a grappler, but the ship was free and angled for an attack. Chakotay ordered a full spread of photon torpedoes to be fired at the Vidiian ship, neutralising the threat. ()
Another enemy Voyager faced in the first year were the Komar. Chakotay's shuttlecraft was attacked by them during an away mission. After the attack, Chakotay was apparently rendered brain dead, forcing The Doctor to use artificial means to keep his body alive. In reality, however, his neural energy had been extracted, turning him into a disembodied spirit, while Tuvok – who had been in the shuttlecraft with him – was possessed by the Komar in an attempt to lure the crew into a nebula and steal their neural energy. Although Chakotay soon learned how to control others in order to prevent the crew being led into the trap, his actions were initially taken as being the actions of a hostile entity trying to sabotage the ship. However, Chakotay's presence was confirmed when he ejected the warp core after having occupied B'Elanna Torres' body: she lacked the authority to eject the core by herself, but, as first officer, Chakotay possessed the required command codes. With his presence confirmed, he subsequently used a medicine wheel, which that Torres had placed in sickbay next to his body, to provide the crew with a map out of the nebula. The Doctor later developed a treatment that returned his mind to his body. ()
Another time, Chakotay, Kim and Tuvok were held hostage by a photonic lifeform because one of the lifeform's fellows was contained on Voyager for scientific tests. The crew are released when the lifeform is. ()
The first officer's bravery is demonstrated when, disguied as a Vidiian, one of Voyagers most feared enemies, he infiltrates a Vidiian labor camp and medical facility to rescue Torres and Paris. ()
==== The second year (2372) ====
Early on in the second year, Voyager visited a planet where Humans lived. The inhabitants invited any of Voyagers crew to stay with them. Both Janeway and Chakotay were saddened by the prospect that members of the crew might stay behind and concerned about how hard it might become to run a starship with a diminished crew. Chakotay reassured Janeway, however, saying, "No matter what happens, we'll make it. Remember that". It turned out that not one crew member decided to stay on the planet. ()
While honoring one of his tribal rituals, remembering the anniversary of his father's death, Chakotay's shuttlecraft was attacked by a young Kazon of the Ogla sect seeking to earn his Ogla name through killing. Chakotay outmaneuvered the Kazon and destroyed his ship before beaming the child to his own. The young Kazon, called Kar, was angry at Chakotay because being taken captive and either not being victorious or dying in battle were a disgrace. Chakotay's shuttlecraft was captured by Kar's sect's main ship and the Kazon-Ogla First Maje said Chakotay could go free if he killed Kar. Throughout his time with Kar, Chakotay had insisted that he wasn't interested in a fight or in killing people and he refused to kill Kar, instead taking the First Maje hostage and escaping with Kar's help. Chakotay continued to refuse to kill, ignoring Kar's information about how to destroy the Kazon ship, and Kar eventually realised that Chakotay wasn't his enemy. When the pair were eventually caught, Chakotay had devised a plan to enable Kar to return to his sect with honor: he told Kar to kill him, and he would then be beamed to sickbay on Voyager where he would be resuscitated. In the moment, however, Kar, unwilling to kill Chakotay, killed the First Maje and regained his place in his sect. ()
When The Doctor's program was damaged while he was in a holo simulation in the holodeck and he was experiencing delusions that were telling him he was really a Human trapped in a simulation on Jupiter Station, he was in danger of destroying his program by terminating the simulation. Chakotay was projected via a hologram into the simulation and tried to explain to The Doctor what was happening. Trying to convince him to terminate the simulation, his delusions asked him what he would rather be: a Human with a real life and family or a hologram trapped in a sickbay on a ship lost in deep space. Chakotay informed him that what he was made of didn't change who he was to the rest of the crew: he was their friend and no less real than anyone else. He manged to delay The Doctor long enough for the crew to work out how to free him from the simulation without terminating his program. ()
Chakotay's interest in anthropology became useful again when, during the second year, Voyager was attacked by a spaceborne alien of similar dimension to the ship. The alien saw Voyager as a mating rival. While Janeway is preparing to attack the alien in return in an attempt to escape, Chakotay, having observed how smaller members of the species behave in deference to the larger, recommends Voyager mimics them to appear less threatening. Chakotay's plan is successful. ()
Chakotay had a frustrating period in command when Voyager was being distorted by an unknown force that didn't respond to any of their attempts to reverse it. Janeway had been incapacitated by the force, leaving Chakotay in command. During these events, Chakotay vehemently opposed a challenge to his command from Tuvok but, when they thought they were possibly going to die, Chakotay tells Tuvok that, while he does find him to be arrogant at times, he can't deny that he's an excellent officer. Tuvok, in return, admits that he has had difficulty accepting Janeway's decision to promote Chakotay to first officer over him and apologizes for anything he did to make him uncomfortable. The force warping Voyager turned out to be a lifeform trying to communicate with them and the ship returned to normal once it had moved on. ()
While stranded on a planet during an away mission, Chakotay came in contact with an alien race that spoke the language of his ancestors. The aliens explained that they had visited his ancestors over 45,000 years ago, gave them a genetic bonding and were known to the tribe as the Sky Spirits. When they eventually returned to Earth on their last trip, finding no trace of the tribe, they believed they had been wiped out by other Humans. 
When Chakotay met and spoke with the Sky Spirits, he was finally able to feel the kind of connection to his heritage that was always missing when he was younger. He wished that he could see his father's face now in this moment of epiphany. He explained to the aliens that Kolopak had died fighting for his colony, honoring the land just as he always said he would and just as his ancestors had done. During this encounter, Chakotay finally came to truly understand his father, telling him in spirit that he could finally hear the sky spirits. () 
Chakotay and Janeway's relationship was tested when Chakotay left Voyager without permission to pursue Seska and the Kazon on his own in a shuttlecraft. With Seska's help, the Kazon had successfully raided Voyager and stolen transporter technology – technology that was unique to their part of the quadrant and with which they could dramatically change the balance of power in their favor. Janeway had decided Voyager would retrieve the techonology; however, while all the crew had been beaten by Seska, Chakotay took it personally, Seska having deceived him a number of times in the past, which ended up humiliated him because he had defended her. Chakotay's daring mission to destroy the stolen technology – using Maquis tactics he had learned from Seska – was successful, but left him stranded with the Kazon and put Voyager in danger when they rescued him (he had asked that they abandon him, a suggestion that was seriously considered by Janeway; she decided against it following an intervention from Torres, who said it would badly effect the crew if they left him). Chakotay was put on report, Janeway asking him, "How do you expect me to keep order when the first officer decides to run off like some cowboy because he believes it's a good idea?". Chakotay also received shocking news from Seska following his encounter with her: she said Chakotay was going to be a father because she had extracted some of his DNA and impregnated herself with it. (It turns out Chakotay wasn't the child's father, something he only learned months later – which, when discovered, was a surprise to Seska.) ()
The same year, Chakotay and Janeway were infected with an incurable virus which necessitated them being left behind on a planet whose environment somehow halted the progression of the disease. They named the planet New Earth and, while Janeway was not willing to give up on a cure, Chakotay came to terms with their predicament and worked on making the planet a better home. He even built Janeway a bath tub. During their time together, they drew closer and Janeway asked him to drop the formalities and call her Kathryn. The first signs of affection between the two also began to manifest as outside of a command structure a romantic relationship seemed less inappropriate, but both were still hesitant to act on their feelings. After an antidote was found for the disease and they returned to the ship, they decided to leave everything that had happened on the planet between them behind and maintain a professional relationship which eventually developed into a deep friendship between the two. The one thing that remained of this time was his continued use of her first name, an intimacy never granted to anyone else on board Voyager. ()
==== The third year (2373) ====
After Voyager traveled back in time to 20th century Los Angeles on Earth to stop Henry Starling from stealing the timeship Aeon, Chakotay had a conversation with Torres about what they would be doing with their lives if they were stuck in the 20th century. Chakotay said that he could see himself pursuing archaeology full-time, teaching at the university or working in Central America, making important discoveries and maybe even winning the Nobel Prize. The crew were successful in stopping Starling from taking the timeship into the future on a poorly calculated journey that could have triggered a temporal explosion. They were then returned to the future they had come from, in their previous location in the Delta Quadrant, by a Federation officer piloting the Aeon from a now saved – and oblivious to the narrowly missed disaster – 29th century. ()
Later that year, he was injured during an away mission and trapped on a world where the inhabitants were engrossed in conflict. While recovering from his injuries, among one of the people who rescued him was a Human named Riley Frazier who, as it soon turned out, was a former Borg drone severed from the Collective, as had all the inhabitants on the planet. She explained that five years ago, their Borg cube was damaged by an electrokinetic storm and their link to the Collective severed. They moved to the planet but unfortunately, as soon as people began to assert their identities, conflicts erupted, and people turned against each other. Some, like Riley and her companions, were not interested in fighting but wanted to work cooperatively. They asked Chakotay to help them by activating the neuro-electric field generator in the Borg cube so that they could reconnect the entire population. Riley explained that the link would provide them with the unique ability to cooperate and problem-solve so they would be rid of conflict and instead could finally create a safe and productive community. Chakotay passionately advocated for Riley, but Janeway found it unconscionable to reactivate the cube. Pretending to have respected Janeway's decision, Riley and her friends – who had previously linked with Chakotay to heal his severe injuries – used the residual effects of the link to telepathically connect with him again and force him to reactivate their link. After Chakotay reactivated the cube, he was let go and the cube – as promised – was destroyed by the New Cooperative. Chakotay was somewhat disappointed with what they had done, stating that even though they held their part of the bargain, they did not hesitate to impose their collective will on him when it served their purposes. He wondered how long their ideals would last in the face of that kind of . ()
The same year, Chakotay became involved in the Distant Origin Theory controversy among the Voth, a species that believed they were native to the Delta Quadrant. Forra Gegen, a leading Voth scientist and (like Chakotay) paleontologist, believed that the Voth were descended from a species in a different part of the galaxy: Earth. The official interpretation on the planet was that the Voth were the first beings to evolve into intelligent beings in the galaxy. After finding the bones of a Voyager crewmember, he believed that he had evidence of his theory. He discovered Voyager, and, using a cloaked device, boarded the ship, abducting Chakotay. The Doctor determined that the Voth had evolved from the dinosaurs on Earth. When the evidence was presented to the Voth council, Chakotay stood with Gegen to support his evidence and spoke persuasively. The council rejected the evidence and threatened to imprison Chakotay and the rest of the Voyager crew, unless Gegen publicly disavowed his theory, something Gegen felt he had no choice but to do. Before leaving, however, Chakotay gave Gegen a small hand-held globe of planet Earth in the hope that one day the Voth would see it as their place of origin. As they parted, Chakotay spoke Gegen's moto to him, "Eyes open", which Gegen returned. () 
Chakotay's holodeck image became a central figure in a Tuvok-written holoprogram about a Maquis-led mutiny. In that holonovel – which was originally written for training purposes in case of a mutiny – Chakotay was depicted as a traitor instigating a mutiny against Captain Janeway and the rest of the Starfleet crew in order to get them back home unhindered by Federation rules and principles. While amusing at first, the holonovel quickly turned dangerous when it was discovered that the program had been accessed by Seska before she left the ship and programmed to trap and kill whoever submitted changes to it. ()
That year also proved to be one of the most challenging chapters for Voyager and its crew as they finally entered the much-dreaded Borg space. When they discovered that the Borg were at war with a powerful species known as Species 8472, Janeway decided to enter into an alliance with the Borg for safe passage through their space in exchange for helping them beat Species 8472. Chakotay was strongly against entering into such an unholy alliance, in part because of his experiences of being controlled by a collective using Borg techonolgy, but Janeway was convinced that it was the only option available to them. When the Borg betrayed Janeway, just as Chakotay had predicted, and she was injured, Chakotay took command and broke off the alliance. When Janeway recovered, she was disappointed that Chakotay did not trust her. This incident marked one of the many clashes between Chakotay and Janeway over command decisions. Chakotay was instrumental in defeating the Borg after they try to double-cross Voyager, linking with the drone Seven of Nine via a neural transceiver attached to his neck, communicating with the Human part of the drone before Torres send a power surge to overwhelm the drone. Chakotay was injured in the process. He was extremely skeptical of Janeway's decision to try to integrate Seven of Nine into the Voyager crew. ()
==== The fourth year (2374) ====
In 2374, Chakotay had various encounters with a number of different races. After a shuttle accident, he was brainwashed by the Vori, who had him join their war against the Kradin. They used simulated scenarios of innocent Vori being killed and tortured. Despite the peace he had found and peaceful ways he had learned over the recent years while on Voyager, he became so embittered by the Vori propaganda that he turned into a killing machine. He was rescued by Tuvok and convinced of the brainwashing before he could complete his first real incursion against the Kradin. ()
He and the crew were used in medical experiments by the Srivani. When Neelix was almost killed in an accident and brought back to life, Neelix questioned his beliefs in the afterlife and the meaning of life itself. Chakotay, being a spiritual man himself, urged Neelix to not draw any negative conclusions from his experience but instead see them as a time for growth into a potentially stronger faith. ()
Chakotay saved Voyager from the Dream Aliens: they had caused the crew to remain in a dream state while they were attempting to destroy the ship. Chakotay used lucid dreaming in order to remain in control during his dream and thus interacted with the aliens. He managed to wake himself and, with The Doctor's help, stay awake while he worked out how to help the crew. He eventually found that the aliens were using a large transmitter on their home world to boost their dream control to the entire crew. He told The Doctor to aim a torpedo at the cavern and, upon reentering the dream controlled by the aliens, tells the alien leader to end the dream or face destruction, freeing the crew from alien control. ()
Chakotay and his fellow Maquis received bad news this year when Starfleet managed to get messages to Voyager. In a letter from Sveta, the person who had recruited him into the Maquis, Chakotay heard that the Maquis have been defeated and many of his Maquis friends had been killed. Chakotay relayed this to the other Maquis on board. ()
The Hirogen hijacked Voyager during this year and turned the holodecks into a hunting arena, forcing the crew to battle against them in different holo simulations. The crew, with neural interfaces implanted in their necks, believed themselves to be the characters they were playing in these deadly games. In one such simulation, in which the Hirogen took on the role of Nazis during World War II, Chakotay was Miller of the United States Army. Thankfully, efforts to liberate the crew, initiated by The Doctor and Harry Kim, were successful. ()
Chakotay and an alien from an isolationist species fell in love during the course of this year. The problem was, however, that due to their biology 's race, the Ramuran, were forgotten within hours of absence from members of other species. Chakotay didn't remember Kellin upon her return to Voyager, where she sought aslyum from her people, who would try to capture her and return her to Ramura. She had returned to Voyager because she loved Chakotay, specifically because he was kind. Initially unsure of Kellin, having forgotten her after her previous departure, they quickly fell in love again. Unfortunately, a Ramuran tracer boarded Voyager and wiped Kellin's memory of life outside of Ramura, including Chakotay. Chakotay tried to convince her they were in love but failed and sadly said goodbye. Before he forgot, he wrote down his memories of his time with Kellin. ()
Chakotay demonstrated his extensive piloting ability when he landed Voyager on a Demon class planetoid, successfully navigating the starship through its savage atmosphere. Later, on an away mission to look for missing crewmates Paris and Kim, when tricorders weren't able to help he used scouting skills he had learned from his tribe. While on the planet, Chakotay and the crew allowed themselves to be duplicated by a biomimetic lifeform known as Silver Blood. ()
==== The fifth year (2375) ====
Chakotay effectively captained Voyager for months as it journeyed through an area of space seemingly devoid of life and even planetary objects and stars. During this time, Janeway had confined herself to quarters and was suffering from depression brought on because she felt guilty for stranding her crew far from home. Chakotay tries to convince her to resume her duties fully, but she refuses. Later, as Janeway tried to assuage her guilt by ordering the crew to abandon her at one end of a spatial vortex she will destroy once they have pass safely through, Chakotay leads the crew in refusing her orders, forcing Janeway to reconsider and stay with the crew. He informs the captain that he "wouldn't be a fine first officer if I hadn't". Moments prior to the crew's confrontation with the cpatain, Chakotay asked for Tuvok's support in refusing her, which may have been a turning point in their relationship. ()
The news received the previous year, about the defeat of the Maquis and the deaths of their Maquis friends effected the Maquis onboard Voyager in different ways. Months after hearing the news, B'Elanna Torres, who had initially reacted with anger, had become depressed and numb to all feelings in her life and began taking extreme risks in an effort to feel alive: turning the safety protocols off in the holodeck, she would fight Cardassians or go orbital skydiving. When it became apparent that she was unwell, Chakotay tried to help her. Using rather forceful methods – perhaps because he himself was disturbed by one of Torres' holoprograms, which depicted the deaths of their Maquis friends – he made Torres confront her thoughts and actions, reminding her that, while she had lost much of her Maquis family, the crew on Voyager were her family, too, that they would be with her, and that she needed to find other ways to deal with her depression. ()
Chakotay encountered Species 8472 again, when Voyager discovered an Earth-like recreation on a space station. It turned out to be a training facility for a possible invasion of Earth by Species 8472. They had assumed various identities of Starfleet officers. While on reconnaissance Away missions to the station he became romantically involved with one of the aliens who had assumed the identity of a Starfleet commander named Valerie Archer. Their mutual respect and trust were important factors in persuading their superiors to come to a diplomatic agreement to avoid conflict. ()
In 2375, Voyager was able to apparently perfect their own version of the Quantum slipstream drive to get them home. However, a potential glitch in the drive meant Chakotay and Harry Kim had to use the Delta Flyer to map the slipstream in advance of Voyager, monitoring potential instabilities in the slipstream matrix as it formed and relaying corrections back to the larger ship. The night before the voyage, Janeway invited Chakotay to dinner in her quarters, their last night in the Delta Quadrant. When asked, Chakotay expressed doubts about the plan to use the drive, stating that the risks were so high Starfleet engineers would not allow it. Janeway said she was willing to take the risk and asked if Chakotay was with her. "Always", he replied. Chakotay piloted the Flyer while Paris was at Voyagers helm. The drive destablised shortly into the voyage and did not return the ship to the Alpha Quadrantc, although it did knock ten years off the journey. ()
It was this at point, more than a year since Seven of Nine had been severed from the Borg Collective and joined the crew of Voyager, who were now at risk of losing her to an illness, that Chakotay expressed to Janeway that she had proved him wrong regarding her decision to integrate Seven into the crew. ()
Chakotay's hopes and fears were revealed when Voyager came into contact with a "Telepathic pitcher plant" during this year. The enormous space-dwelling organism inticed the ship into its digestive tract by making the crew believe it was a wormhole home where they would receive their desires. Chakotay imagined he'd received a full pardon for his actions as Maquis and a professorship of Anthropology at Starfleet Academy. ()
Chakotay devised the plan for stealing the Borg transwarp coil from a Borg sphere described by Janeway as "Fort Knox". The heist was successful, except that during the away mission Seven of Nine chose to return to the Collective. Despite his previous steps to acceptance of Seven of Nine, Chakotay was ready to wonder if she had betrayed Voyager. ()
When Voyager became trapped in chaotic space, alien inhabitants of that region communicated with Chakotay by reactivating a medically suppressed, defective gene of his responsible for an inherited cognitive disorder called sensory tremens that could cause realistic auditory and visual hallucinations – which the aliens spoke through, appearing to Chakotay in the faces of his friends, family and a boxing opponent. Chakotay – whose grandfather, Chakotay believed, had become insane because of the gene – was frightened of becoming like his ancestor and resisted the aliens' efforts. Fighting against his fears, he learned from the aliens how to guide the ship out of chaotic space before the ship was destroyed by the anomaly. ()
While bringing up the rear of an away team escaping a depressurising deck on a Malon export vessel contaminated with theta radiation, Chakotay was knocked unconscious by flying debris and had to be beamed out of the vacuum to Voyager. ()
One of the more serious conflicts between him and Captain Janeway occurred in late 2375 with the discovery of the that was commanded by Starfleet Captain Rudolph Ransom. Ransom and his crew had been using nucleogenic lifeforms as fuel for their special warp drive; an act that appalled Janeway unimaginably, especially because it was a dishonor to Starfleet, leading her to set upon a relentless hunt until the Equinox and its crew were brought to justice. In her fury, she not only compromised the safety of the ship on numerous occasions, despite Chakotay's advice, but also wanted to subject one of Ransom's captured crew members to torture to retrieve information out of him. Chakotay was successful at preventing the worst from happening and warned her that he would not tolerate her crossing that line again. Janeway, angered and determined, relieved Chakotay of duty, so she could pursue Ransom unhindered. When she finally came to her senses, she realized how she had crossed the line herself and that Chakotay would certainly have had good reason to have stage a mutiny against her. Chakotay said he had thought of doing such, but that that would have been crossing the line. ()
==== The sixth year (2376) ====
Towards the start of this year, Seven of Nine learned she was responsible for the condition of three members of her former Borg unimatrix whose minds were still linked despite having escaped the Collective. As they lie unconscious in sickbay, she battles with guilt and their fate: to separate them into individuals who will die within a month or return them to the Borg where they will live longer but as part of the Collective. Chakotay tried to comfort Seven, asks her to think about her experience and to consider the difference between existing and living. Seven's decision is that "Existence is insufficient". ()
Voyager was caught in a conflict begun by the Vaadwaur, a confrontational and treacherous species that was revived after over eight-hundred years in stasis. They had been revived by a crew member with good intentions and, as they were unknown to Voyager and seemed in need, Janeway made an alliance with them. Chakotay felt uncertain about the Vaadwaur's intentions and was wary of awakening them, recalling an old Greek myth about a dragon killed in battle whose teeth fell to the ground only to spring up as full-grown warriors to continue the fight. He used this allegory to demonstrate how Voyager might inadvertently be re-instigating a bloody war that had long stopped. ()
In the same year, Voyager encountered an ancient spaceship from one of Humanity's first manned missions to Mars floating in a gravimetric distortion. Chakotay instantly recognized the phenomenon, recalling how the Ares IV was lost to it in the early 21st century. He was intrigued by their discovery and more than enthused to be leading the mission to enter the distortion to retrieve the command module. Tom Paris was impressed that Chakotay knew more about the Ares IV than he did. Chakotay remarked that the Mars missions paved the way for the exploration of space and that Lieutenant John Kelly, who piloted the Ares, was one of his favorite childhood heroes. During the away mission, Chakotay also got to engage in another of his interests, paleontology, discovering things contained within the anomaly. Chakotay's obsession with recovering the command module, however, put the lives of the away team at risk. Despite being ordered to immediately leave the distortion because it was becoming too dangerous to stay inside, Chakotay insisted the team haul the module with them, inhibiting their escape and causing them to become trapped. Chakotay was injured when they were trying to leave the anomaly and had to remain on the while the task of retrieving a component from the command module to fix the Flyer fell on Seven of Nine, who did not share Chakotay's or anyone else's enthusiasm for such sentimental attachments to history. Chakotay expressed his envy when he realized that he could not beam on board the Ares and insisted Seven download the data Kelly had recorded. While Seven was angry with Chakotay for endangering their lives, his and the rest of the crew's enthusiasm for discovery and remembering history affected her and she began to appreciate learning about, remembering and being inspired by history. ()
In the same year, when Seven overloaded her Human brain trying to download too much information at once from the ship's logs and became delusional about possible conspiracies aboard the ship, Chakotay and Janeway almost came into conflict when she told them two competing conspiracy theories and they became suspicious of each other. When they discovered what had happened, they realised they had come too far together not to trust each other. ()
When Voyager weathered a neutronic storm the crew filled their time in one of Paris' holo programs. Janeway begins to fall in love with one of the characters but is uncomfortable and embarrased by that. Chakotay, whilst teasing her a little, also encourages Janeway to enjoy the relationship, saying that it's nice to see her having a little fun, sharing that it's something he did with holo programs himself. Janeway took his advice (and that of The Doctor, who advised similarly) and countinued to cultivate a relationship with the holo character. A number of weeks later, when there was a dangerous problem with Paris' program, Janeway wanted to avoid turning off the energy supply to the program, if possible, so the program wouldn't be lost. She said that, while the characters weren't real, the crew's (including her own) feelings for them were. ()
Chakotay's love of anthropology brought vital information to Voyager when it was caught in the gravimetric gradient of a planet on which time passes more quickly than in the rest of space. Chakotay launches a probe that records images every ten milliseconds, enabling the crew to see civilisations develop on the planet and track seismic activity caused by the presence of Voyager. He says the information provided by the probe could be the greatest anthropological find of his career. With Seven of Nine, he was also the first the find and translate a message from the planet's inhabitants. When a difficulty transporting The Doctor back to the ship from the planet's surface meant The Doctor was trapped on the planet for years (by the time frame of the planet) and hard to locate, Chakotay, knowing The Doctor's love of opera and concert music, suggests narrowing sensor scans to the arts district. The Doctor is immediately found. ()
The ship's crew suffered traumatic memories of participating in the massacre of innocent civilians on a nearby planet, believing they had been responsible the atrocity. Chakotay and an away team who first surveyed the planet suffered the most from the memories. At one point Neelix, suffering from these memories and believing himself to be in a firefight, holed himself up in the mess hall and Chakotay had to talk him out of it. The crew discovered the memories were being transmitted by a synaptic transmitter in a structure on the planet that sent neurogenic pulses that caused memories of the massacre to be implanted in anyone who came near. It was a memorial to the victims of the massacre and a reminder to never let such a massacre happen again. Most traumatised, Chakotay and other members of the original away team wanted to dismantle the monument so that others wouldn't have to experience the trauma they had. The memories could not be removed and would always stay with them. Janeway overrulled them, saying that the monument must stand as a testimony to the lives lost. The crew repaiered the structure so that it functioned properly and left a warning buoy orbiting the planet to inform other ships of what to expect. ()
During shore leave on Norcadia Prime, Chakotay and other members of the crew were able to enjoy watching martial combat competitions. Jokingly, he said he was observing it for anthropological research but, being a boxer, he was quite a fan of the local martial art tsunkatse, discussing fighters' statistics with his crewmates. While watching a match, Seven of Nine entered the combat arena, having been kidnapped, along with Tuvok, and forced to fight. Janeway being away from the ship herself, visiting a planet in the neighboring system, Chakotay lead Voyager in finding the ship on which Seven and Tuvok were held and attacked it, despite the ship being stronger than Voyager– in Torres' words, it was "way out of our weight class". As they attacked the ship, Penk, the leader of the kidnappers, commended Chakotay on his fighting spirit. With the help of Janeway returning in the Delta Flyer, they mamaged to extract Seven and Tuvok from Penk's ship. ()
Returning from an away mission in the Delta Flyer, Chakotay is captured by a Borg cube along with Paris, Kim and Neelix. Held in an assimilation chamber, Chakotay manages to keep his team calm, despite their fears of impending assimilation and organizes them to try to find a way to escape. Their efforts are foiled but thankfully they are later rescued by Voyager. ()
Like others of his former Maquis fellows, Chakotay's sense of being Maquis was never lost, even after six years on Voyager. When Starfleet managed to get a message to Voyager and Admiral inquires specifically about the status of the Maquis onboard the ship, Janeway is unsettled by it, saying she has forgotten the former antagonism between Starfleet and Maquis. Chakotay confesses that he hasn't. ()
Towards the end of this year, in response to a request for help against the Borg, Janeway made a plan to inflitrate a Borg vessel and introduce a nanovirus into the Collective. She told Chakotay that, despite having forged ahead in the past without Chakotay's support, she wouldn't follow this through unless Chakotay supported it. Chakotay was unconvinced that Janeway would listen to him even if he didn't support the plan. This time, however, he did support her, seeing it as a potential way to finally defeat the Borg. However, when Janeway planned on infiltrating a Borg vessel alone, Chakotay, believing it too risky, insisted Janeway agree to take Tuvok and Torres with her. Janeway resisted and Chakotay pushed back. Janeway said she thought she had his unconditional support this time; he replied, "This is the best I can do" and indicated he would take measures to stop her from going alone, if he had to. Janeway agreed to take Tuvok and Torres with her, who were invaluable. As they approached the Borg vessel and Janeway went to join the away team, perhaps realising the seriousness of this mission she reached out a hand to Chakotay, who held it as they both stood and Janeway gave command of the bridge to him. When the away team, in the Delta Flyer, was approaching the Borg vessel to board it, Chakotay attacked the Borg, drawing fire to Voyager and weakening the Borg's shields so the away team could teleport inside.
While Voyager waited at a distance for the away team to complete their mission, Chakotay experienced a little of what it must have been like for Janeway with him as her first officer. With Janeway and Tuvok away, Lieutenant Paris was technically Chakotay's first officer, and he approached Chakotay to offer his opinion, as was first officer's duty. Chakotay wasn't immediately interested in listening to Paris who, worried about the away team – especially because his partner, Torres, was part of it – said Voyager should return to the Borg cube immediately to rescue them. Chakotay said they would wait until the away team's mission was complete. Paris, like Chakotay to Janeway, was insistent but overruled by Chakotay, who told him that, for the mission to work, he needed the support of his "first officer", Paris. Paris agreed.
At the right moment, initiating the next stage of the plan, Chakotay commanded Voyager back to the Borg vessel and rescued the away team with the help of an allied ship – and the support of his "first officer". ()
==== The final year (2377-78) ====
Chakotay's identity as Maquis was still present in his seventh year after being taken from the struggle in the Demilitarized Zone. When members of Voyagers crew who were Maquis were being attacked one by one, Chakotay became defensive of them and suspicious of the Starfleet part of the crew. In words that caught both Janeway and himself off guard, he referred to the Starfleet part of the crew as "your [i.e., Janeway's] crew", correcting himself when called up on it. He organised the Maquis to work in pairs and to carry sidearms. It transpired that the attacks were being carried out by Tuvok, who, during his time undercover in the Maquis, had had supressed memory commands implanted into him, and now activated, by Bajoran fanatic Teero Anaydis. During the attacks Tuvok mind melded with the Maquis and implanted in them the command to mutiny. Under this mind control, Chakotay and the other Maquis whom Tuvok had attacked successfully hijacked Voyager until Tuvok, awakened by Janeway, performed another meld with Chakotay to free him from Anaydis' influence. ()
When The Doctor betrayed Voyager and joined a group of holograms intent on liberating other holograms from organic species and setting up their own homeworld, Janeway believed his program must have been tampered with by the holograms. Chakotay, perhaps because of his experiences joining the Maquis, suggested another possibility: that The Doctor "may have done what he did because he genuinely believes in their cause" and that maybe he had started thinking of the other holograms as his family. As it turned out, Chakotay's perception was correct, but Janeway was unwilling to believe it or that the holograms should be regarded as people. Later, Chakotay piloted the Delta Flyer through the atmosphere of a Class Y planet, with Paris and Tuvok in tactical support, and attacked the holograms' ship, saving Torres, The Doctor and five Hirogen from them. When back on Voyager, Janeway is lenient with The Doctor, feeling partly responsible for his development into someone who could make mistakes, and counts his time with the holograms as an "away mission". ()
Twice around this time in the journey, Chakotay approached Janeway with Tuvok to express the same concerns they had about possible actions the captain might take. Once, they approached her when she wanted to make an alliance with the Hirogen to find the holograms The Doctor has joined – Tuvok was concerned about the security risk; Chakotay questioned the level of responsibility they had towards this potentially dangerous mission. A few months later, they approached Janeway when she wanted to make an alliance with other ships who were trapped with them in an area of space devoid of stars, planets, or any other source of energy. They both wondered whether Voyagers tactics should rather be like that of the ships that have survived in the void for years: to take supplies from other ships. Janeway overruled them both both times: the first time because she felt partly responsbile for the holograms because she had been the one to give the technology to the Hirogen; the second time because of her committment to Startfleet principles. ()
Chakotay's trustworthiness and respectability – and the vital nature as a unifying presence on the ship – was shown later that year when he restored Voyager to its proper timeline after it was hit by a chronokinetic surge from a spatial rift that shattered the ship into 37 different timeframes separated by temporal barriers. Some of the timeframes were from before Voyager was in the Delta Quadrant, some up to 17 years into Voyagers future. In order to fix the timeline, Chakotay had to convince members of the crew – most importantly, Janeway, who was from the time they were still enemies – of their predicament and to work together. The task was made harder by the presence of Seska in one of the timeframes, who was working against him yet again. When Janeway realised she might be able to stop Voyager from ever getting trapped in the Delta Quadrant, Chakotay convinced her not to change the timeline, for the sake of all the positive things that had happened to Voyagers crew over the past six years – for example, the liberation of Seven of Nine. When he had finished convincing her, Janeway asked him if, in their shared future, he always lectured her like that, to which Chakotay replied that she needn't worry, she would always have the last word. Chakotay made such an impact on Janeway that, as the parted, she asked if their closeness had ever become romantic. Chakotay said that there were some barriers that they never crossed. When the timeline was restored, Chakotay diverted all of Voyagers power to its deflector system and setting it to a specific frequency, thus using the deflector array as a lightning rod for the energy surge from the spatial rift, burning it out, but avoiding the timeframe shattering. Due to the Temporal Prime Directive, Chakotay, the only one who knows what's happened, couldn't tell anyone about it and Janeway and the crew have to trust him, which they readily do. ()
B'Elanna Torres became pregnant this year, which made Chakotay happy. When Torres was annoyed that people were offering parental advice all the time, Chakotay was there for her, offering some normality, which she appreciated. Chakotay suggested himself as the child's godfather, an offer Torres declined, choosing The Doctor instead, in part because she believed Chakotay didn't really know about raising children. ()
While on an away mission with Kim and Neelix, the rest of the crew were kidnapped and made to work on a planet with a labor shortage. The crew were brainwashed so that they could not remember their past and believed they had lives on the planet. Chakotay and Neelix carried out reconnaissance on the planet, Chakotay assuming the false identity of Amal Kotay and working in the factory where many of the crew were. Together, they managed to liberate Torres, but Chakotay, injured by guards, became trapped on the planet, a fugitive. He then tried to convince Janeway of who she really was, but she turned him over to the authorities. Chakotay appeared saddened when he learned that Janeway was falling in love with someone who lived on the planet. Once caught by the authorities he was brainwashed and order Voyager to return to the planet, where it was ambushed. Thankfully, the skeleton crew were able to escape and Chakotay had done just enough to help his brainwashed crew mates begin to question their situation on the planet, find each other and expose those who are performing the brainwashing. ()
After Starfleet worked out a way to communicate with Voyager on a regular basis, they gave the crew their first official mission in seven years: to find Friendship 1, a deep space probe launched by the United Earth Space Probe Agency in 2067 with the purpose of finding other species. The last known location of the probe was close to Voyagers route and, after tracing it to a seemingly uninhabited planet, Chakotay lead an away team to retrieve the probe. It turned out the planet was inhabited – by people who had suffered a devastating disaster after using the technology they learned from Friendship 1, and they blamed Humans for it. The inhabitants attacked the away team and Paris, Neelix and Joe Carey were taken hostage and Carey was murdered. Chakotay and Kim had to retreat from the planet. Later, Chakotay returned with an away team to rescue the remaining hostages. Dispite now not being compelled to help the planet's inhabitants (because the hostages had been rescued), Voyager reversed the worsed effects of the disaster before resuming its course. ()
On the way to a scientific conference on Ledos, Chakotay and Seven of Nine became stranded under an energy barrier on the planet's surface after their shuttle crashed into it. The barrier protected a primative people, the Ventu, from the other inhabitants of the planet but needed lowering in order for Chakotay and Seven escape. Chakotay was fascinated by the Ventu from an anthropological perspective but he and Seven kept their distance because of the Prime Directive. However, Vendu found Chakotay as he rested under a tree, his leg injured during the crash. While with them, he received their hospitality and medicine and learned some of their language. He became concerned about the influence his presence was having on them, however, after members of the tribe started imitating him and incorporating scavenged parts of the shuttle into their dress. Finding themselves with no other choice, Seven and Chakotay asked the Ventu to help them move a large part of the crashed shuttle so it could be positioned correctly and adapted to lower the barrier. They managed to get in contact with Voyager and returned to the ship where they talked about what they thought would now be best for the Ventu: Chakotay advocated for restoring the barrier to allow the people to carry on living undisturbed by those outside; Seven, while concerned that a culture might be lost, suggested that maybe the outside influence could help a resourceful and intelligent people develop positively. Chakotay questioned how she might know what it best for the people. Janeway agreed with Chakotay, and the barrier was raised. ()
Chakotay was the first to realise things weren't right after Janeway returned from a trip with The Doctor. She was acting unusually and being secretive and Chakotay suspected someone might be impersonating her. He invented a story about her past, mentioning it to her, and when Janeway acted as if it was something that had happened, he knew it wasn't really her. He tried to contact security but was overpowered, sedated and hidden in the morgue. It transpired that The Doctor was the one impersonating Janeway, who had been kidnapped by two Overlookers when she was travelling back to Voyager in the Delta Flyer with The Doctor. The Doctor kept this secret from the crew for fear for the captain's life and was attempting to outwit the crew and take Voyagers warp core to the Overlookers in exchange for Janeway. Thankfully, Tuvok and Paris were able to attack the ship Janeway was hostage on and bring her back to Voyager. ()
During the visit to Ledos a few months previously, Chakotay and Seven became closer. Seven had been attracted to Chakotay for some time but had never told him. Prior to the trip to Ledos, Chakotay had expressed interest in Seven, but very gently, inviting her to a social event hosted in the mess hall. Their closeness increased over the last few months they were in the Delta Quadrant, and they became romantically involved with each other. Seven of Nine tried to end the relationship, however, when she learned that Chakotay's growing love for her could cause him pain should she be injured or killed – a pain she didn't want to inflict on him. Chakotay argued with her, reassuring her that the only thing that was certain in the relationship was the love they felt in the present, not a potential future event. ()
==== The return home ====
It was during this time that Admiral Janeway arrived on the ship and helped Voyager return to the Alpha Quadrant. Unsurprisingly, Chakotay got on well with the Admiral, joking together as they worked. Admiral Janeway had come from what was to become an alternative future. For her, Voyager had taken a further 16 years to get home, experiencing tragedy along the way, and she had traveled back in time to help Voyager get home quicker. Admiral Janeway wanted to avoid the tragedies, but her plan was risky, involving traveling through a nebula with high Borg activity. Chakotay trusted the Janeways could be successful, though, telling Seven, "Our chances would be good with one Kathryn Janeway on the bridge, but with two, I'd bet on this ship any day". At one point, the crew felt deceived by Admiral Janeway, who hadn't told them they would be using a Borg transwarp hub to get home (they believed they'd be using a wormhole). Captain Janeway said they should destroy the hub because it would stop the Borg traveling and assimilating people so easily, saving lives, and Voyager would continue on its route through the Delta Quadrant. The whole crew, including Chakotay, were behind her, recognising the family they had on the ship and the value of the journey. Thankfully for them, the two Janeways devised another plan, involving Admiral Janeway sacrificing herself to blow up the Borg in the hub, allowing Voyager to use traverse the transwarp conduits home, destroying the conduits along the way. ()
==== The Kazon ====
Chakotay became one of the central figures in the conflict with the Kazon. One of the first encounters took place during the time he was performing the Pakra, a ritual to honor his father's death. A young Kazon, Kar, who was being initiated as a warrior, attacked him while he was alone in the shuttlecraft performing the ceremony. Chakotay destroyed his ship, and both were captured by the Kazon and condemned to die. After escaping their death sentence, Kar killed the maje and was proclaimed a warrior, thanks in part to Chakotay's help. However, Chakotay was warned that next time he met the Kazon, they would not be as lenient and kill him. His next meeting with the Kazon also was a reunion with Seska, who had defected to the Kazon-Nistrim, led by Maje Culluh. They had stolen a module that enabled them to penetrate Voyagers shields. Chakotay was able to board the Kazon ship and destroy the module; however, he was captured and tortured by the Kazon. He was rescued by Voyager, but shortly thereafter, Seska told him that she had extracted his DNA and impregnated herself with it. ()
During a constant series of attacks on Voyager by the Kazon, Chakotay suggested to Captain Janeway that Voyager form alliances with some of the Kazon factions and others in the quadrant. This failed when the Trabe, the Kazon's enemies, under the guise of cooperation with Voyager and the Kazon, attempted to assassinate the Kazon leaders at a conference and otherwise didn't show much interest for diplomacy and building coalitions. ()
Shortly after that, Chakotay received a message from Seska that she had given birth to his child, and that Culluh planned to kill her and take the child. Conflicted as to whether he should accept this child into his heart and life given that it was conceived against his will and through deception, he sought the wisdom of his father through a vision quest. In his vision, his father appeared to him saying that the child knows nothing of deception, that it is innocent and that Chakotay must accept him just as centuries ago his ancestors accepted the children of the white conquerors who had forced themselves upon their women; one of whom was a direct ancestor of theirs. Chakotay recognized the wisdom in his father's words and decided to go find his son. Although Seska was not trustworthy, Janeway agreed to try and help him. It turned out to be a trap, however, and Voyager ended up being captured, and the crew stranded on a barren planet with nothing to survive on while the Kazon took the ship and left. Chakotay's knowledge of nature and his Maquis training helped the crew survive. He rescued Kes from the primitive tribe that inhabited the planet. He also helped the crew to elude an enormous eel-like creature that lived inside a cave that they sought shelter in by sealing off the opening as they exited. He also won the friendship of the tribe when he saved one of them from a lava flow. The crew was eventually rescued by Tom Paris, The Doctor and Lon Suder and returned to Voyager to resume their course home. ()
==== Conflict with the Borg ====
In 2373, he encountered a group of former Borg drones, who, due to an accident in space, were released from the Collective and attempted to regain their original identities. Chakotay was seriously injured on this away mission. The group, headed by a Human called Riley Frazier, still maintained the ability to link. They used their link to help heal Chakotay. Frazier told him that there was another group of former drones with whom they were in conflict. She wanted Voyager to help her activate a neural transmitter on the disabled Borg ship so they could link with the dissenting group to establish cooperation and peace in their colony. Janeway refused, so the group used its former link with Chakotay to activate the transmitter. ()
This neural link proved beneficial when later that year, Voyager formed an alliance with the Borg. In exchange for right of passage through Borg space, the crew of Voyager agreed to help them fight Species 8472, who were destroying the Borg. Chakotay was against the alliance and he and Janeway had a fundamental disagreement over how to approach the Borg. Chakotay believed her decision to be foolish at best. He did not trust the Borg and believed Janeway made a fatal mistake of entering into any kinds of agreements with them and expecting to come out alive. On numerous occasions he opposed her, believing she was not only underestimating the enemy but that she was also selfish for wanting to arm the Borg with such a powerful weapon. Janeway was disappointed at Chakotay's perceived lack of trust in her, but he remained adamant, stating that safe passage through Borg space was not worth the devastation that would be unleashed on them after the Borg were equipped with such a powerful weapon. After Species 8472 was defeated, the Borg, as predicted by Chakotay, broke the agreement and attempted to assimilate the crew. Chakotay used his neural link ability to sever Seven of Nine, the Borg drone in charge, from the Collective, thus allowing Voyager to escape assimilation by the Borg. ()
In 2375, Chakotay and Janeway devised a plan to steal a transwarp core from a Borg ship. When Seven was captured, Janeway lead an away team to rescue her. Chakotay, in command of Voyager, attacked the Borg conduit, destroying it. ()
He was also once captured by a Borg ship piloted by child Borg drones that were separated from the collective when the elder Borgs died due to a mysterious illness. With the aid of Seven, he was rescued. ()
=== USS Protostar ===
==== Original voyage ====
Sometime after he and Voyager returned home to Earth, Chakotay officially rejoined Starfleet. By 2382, he had been promoted to captain and given command of a prototype starship, the on Stardate 59749.1. () Before departing on a return mission to the Delta Quadrant, Chakotay was reunited with Janeway, now a vice admiral, during the traditional christening of the Protostar. As Janeway refused to explore the Delta Quadrant again, Chakotay had an advisory hologram made in her likeness integrated to the ship's systems. ()
During its mission, the Protostar entered a temporal anomaly, ending up on Solum decades in the future, where they encountered the Vau N'Akat, a species that blamed the Federation for a civil war which devasted their homeworld fifty years after the Federation made first contact with them. Chakotay attempted to send a distress call, but the damaged ship was then stormed by Drednoks and Chakotay was captured alongside his first officer Adreek-Hu on the bridge. The two officers eventually escaped but were unable to disarm a weapon called the living construct that was placed inside the Protostar nor board the ship to escape. () Chakotay spent months in Vau N'Akat custody, losing his entire crew except for Adreek and using a tricorder that Adreek had managed to hide to send distress calls into the anomaly. () As a last resort, Chakotay remotely sent the crewless ship back through the anomaly to prevent the Vau N'Akat from using the weaponized Protostar in their plot to destroy Starfleet before it makes first contact with Solum. () Before launching the ship, Chakotay included a goodbye message to Janeway, asking for whoever found the ship to get it to his old friend. ()
By 2383, the Protostar was stranded on Tars Lamora, with Chakotay and his crew trapped in the future following the collapse of the anomaly over Solum. () Without news from the Protostar, Janeway mounted a rescue mission and chased after any clues regarding her friend's fate with the . The Protostar was recovered by a ragtag crew of six young aliens, with both Vau N'Akat operatives and Janeway's Dauntless chasing them. () After unlocking an encrypted part of the ship's systems, the crew found a recording of a distress call by Chakotay made just before the ship was boarded. () Having discovered the living construct onboard and its nefarious purpose, Chakotay's successors avoided contact with the Federation to prevent infection. Eventually, Janeway learned of Chakotay's predicament from while on the Protostar. After Janeway restored her holographic counterpart's corrupted program, Hologram Janeway's memories returned and she showed the real Janeway a recording of Chakotay's distress call and the ship being boarded, but the hologram admitted that she didn't know what had become of him. ()
The plot of the Vau N'Akat was ultimately thwarted when Hologram Janeway sacrificed herself and the ship to destroy the living construct. In the process, she intentionally created a new temporal anomaly and a second distress call from Chakotay was thus able to pass through from 2436, confirming that he and half of his crew were still alive in an alternate future. Starfleet discussed sending an exploratory mission to find Chakotay which Janeway decided to lead herself. () They also recovered the Protostars black box with security footage of Chakotay launching the ship and his message to Janeway. ()
Starfleet built the to rescue Chakotay and spent the next six months monitoring the wormhole, discovering that time passed at the same rate on both ends and that it connected to Solum before Chakotay sent the Protostar into the past. As a result, they were forced to wait until the ship's launch before sending the message. With Starfleet Command concerned about the possible ramifications of such a mission, Janeway had to fight to keep it alive, operating from the , the successor to the , the ship that she had captained with Chakotay. ()
However, a rescue attempt accidentally altered history. Dal R'El, Zero, Rok-Tahk and Maj'el attempted to help ensure the launch of the Protostar by Chakotay and Adreek-Hu, planning to rescue them afterwards. In the melee, Dal accidentally dropped his disruptor which allowed Chakotay and Adreek to escape in the Protostar instead of sending it through the wormhole on autopilot. This resulted in the ship not reaching Tars Lamora, changing history. ()
==== Marooned ====
Arriving in around 2374, Chakotay and Adreek ejected the ship's proto-core and antimatter and landed on an island on Ysida, a Class P planet where they were left marooned. Having lost his entire crew, Chakotay was left a broken man with no hope and rejected his first officer's ideas about using the lightning from the planet's ion maelstroms to gather more antimatter. Adreek left to test out his theory on his own and never returned, breaking Chakotay even further. Chakotay was left marooned in a ship powered only by emergency power cells with only for company and his Runaway eventually breaking down. ()
Ten years later, Dal R'El, Rok-Tahk, Jankom Pog, Gwyndala, Murf, Zero, and Maj'el found Chakotay and the Protostar with the help of Wesley Crusher, needing to send the ship back in time to Tars Lamora in order to fix the broken timeline. Chakotay rejected their attempts to enlist his help and mostly ignored the crew until Dal disappeared in a storm. Using the Runaway, which Jankom had repaired, Chakotay led a search for Dal and found himself bonding with the kids. It was discovered that Dal had found Adreek's body near a device which the first officer had used to collect compressed antimatter for the Protostar. Realizing that his old friend had been right all along, Chakotay was filled with new hope and agreed to work with the crew to get the Protostar off of the ground. ()
Needing deuterium gas from a maelstrom across the ocean, the crew converted the Protostar into a sailing ship that Chakotay dubbed the HMS Protostar. Chakotay and Dal, having both been captain of the Protostar, clashed a few times, but Dal eventually opened up to Chakotay that he was unsure of his future anymore. In turn, Chakotay told Dal that he had been searching for purpose his whole life and finally found it as the first officer of Voyager where, although Chakotay wasn't in charge, his role was to support Janeway in whatever way he could. After Dal saved Chakotay's life when he fell overboard, the two set aside their differences completely and Dal settled into the role of something of an unofficial first officer to Chakotay. The refueling proved to be successful, restoring impulse engines and warp drive, allowing the Protostar to finally leave Ysida. However, the was 3,000 light years away, meaning that the crew had to get the protostar drive back online to meet up with Voyager. ()
The Protostar visited a Class M planet in search of the bosonite that they needed to create a new protostar core for the ship. Following an encounter with Klingon scientist and mutated tribbles, they successfully got the bosonite and created a new proto-core for the ship. ()
The Protostar made a proto-jump to Voyagers position, but the proto-warp fractured the already weakened fabric of the universe, splintering Voyager into several alternate realities, including the mirror universe. Using the 's deflector dish, the crew managed to seal the rift and restore reality to normal. Sent to the correct version of Voyager, Chakotay was finally reunited with Janeway for the first time in over a decade. ()
==== Sending the Protostar to the past ====
Although he was welcomed back to Starfleet, Chakotay and Janeway were informed that their orders were to take the Protostar back to Earth where the Department of Temporal Investigations would handle sending the ship back in time and everyone else would be reassigned out of fear that they were too close to the situation. Chakotay and Commander Tysess both reluctantly agreed with this, but an attack by Asencia's forces with temporal weaponry changed things. Needing to ensure that the Protostar remained intact, Chakotay returned to his ship, officially enlisting the young cadets as his crew and Gwyn as his acting first officer, although Dal remained behind to fight with Maj'el and Nova Squadron and Zero stayed to help the injured on Voyager. Although both ships were nearly destroyed, Nova Squadron managed to destroy the Rev-1 using its own weapon and the Boothby Supernova and Zero lost their physical form helping, forcing Zero to get a new containment suit. Afterwards, Starfleet ordered both ships to Solum to stop Asencia and her new weaponry. ()
Gwyn convinced the command staff to send her and the young Protostar crew, who were not officially Starfleet yet, to Solum to rescue Ilthuran and find out the source of Asencia's weaponry. However, while the kids succeeded in rescuing Ilthuran and Wesley Crusher, they were taken captive themselves. ()
Chakotay presented Janeway with a gift commemorating fourteen years since her first command before they received news of Ilthuran and Wesley's arrival. Janeway decided to launch a rescue mission, accompanied by Chakotay, The Doctor, and Wesley. Using a ship replicated by Hologram Janeway to Ilthuran's specifications, the four managed to save Dal's crew from execution. Although Starfleet wasn't supposed to get involved in the brewing civil war on the planet, both Janeway and Chakotay agreed to help save Solum and send the Protostar back in time. ()
With Asencia using her wormhole technology to launch an attack on the Federation at large, Voyager and the Protostar attacked to buy Dal, Jankom, Gwyn, and Murf time to open a wormhole to send the Protostar through to Tars Lamora using Asencia's technology as Rok, Maj'el, and Wesley figured out the specifics. With the aid of the other Vau N'Akat, Gwyn defeated Asencia and Dal, Jankom, and Murf succeeded in opening the wormhole. closing the others on Asencia's fleet, destroying it. However, the Loom appeared to begin consuming everything due to the effects of the paradox. With Voyager providing covering fire, Chakotay and his crew successfully piloted the Protostar into the wormhole leading to Tars Lamora in the past, closing the temporal causality loop and restoring the broken timeline. Chakotay had The Doctor copy Hologram Janeway's program to an EMH backup module so that it could be saved from future destruction before Hologram Janeway's program was reset in order to erase her memories. Voyager beamed the crew out and left the Protostar to finish its journey on autopilot to eventually be found by Dal and his crew. ()
=== USS Voyager-A ===
With Janeway deciding to go into early retirement, Chakotay became the new captain of the . However, the Attack on Mars resulted in Starfleet sending Chakotay to bring Janeway back. Alongside The Doctor, Janeway and Chakotay gave the young crew of the Protostar field commissions as ensigns and assigned them to the new , now a training ship. When Dal R'El chose to serve as acting first officer rather than acting captain, Chakotay visibly approved of his decision. ()
==Alternate timelines==
During the "Year of Hell" conflict with the Krenim, Chakotay advised Janeway of the option of the crew abandoning Voyager and traveling through Krenim space in smaller groups. Janeway dismissed the idea and Chakotay was somewhat relieved. Later, Chakotay was captured by Annorax, the commander of the Krenim ship, along with Tom Paris. At first, he helped Annorax, who promised to return Voyager intact to its original timeline if Chakotay gave him enough detail about Voyagers time in Krenim space, so that Annorax could have the right calculations to use in his time weapon. But after Annorax destroyed a species to try to restore the timeline, Chakotay was convinced to help Paris sabotage the ship by transmitting its location to Voyager and taking its weapons offline. This allowed Janeway to crash Voyager into the Krenim time ship and through its destruction restore the timeline. ()
In 2375, Voyager was able to apparently perfect their own version of the Quantum slipstream drive to return home, but a potential glitch in the drive prompted Chakotay and Harry Kim to use the to map the slipstream in advance of Voyager to monitor potential instabilities in the slipstream matrix as it formed. Due to Kim's miscalculation, Chakotay and Kim were the only two people to make it back to Earth while Voyager crash-landed on a Class L ice planet in the Beta Quadrant, killing all aboard. Fifteen years later, Chakotay had formed a relationship with Tessa Omond, who accompanied him and Harry when they stole the Flyer and certain Borg components from Starfleet before setting out to find Voyager, salvaging The Doctor's program and Seven's corpse with the goal of sending modified slipstream calculations back to before Voyager was destroyed so that the ship could make it home. According to Kim, because of their actions, stealing from Starfleet, and their plans to break the Temporal Prime Directive, Omond, Kim and Chakotay were the most wanted criminals in the galaxy. Despite being pursued by Captain Geordi La Forge and his ship, who damaged the Flyer causing it to suffer a warp core breach, Chakotay was able to buy enough time for Harry to send modified calculations back to Voyager that would disperse the slipstream entirely, stopping the flight before it could reach Earth but cutting ten years off their journey home. As they prepared for the completion of their plan, which would erase the previous 15 years of history – including Omond and his relationship – Chakotay had momentary second thoughts because he loved Omond. Omond reminded him, however, that his heart had always be on Voyager and hoped that perhaps they might still meet in the unwritten future should their plan succeed. ()
==Personal interests==
Chakotay didn't use the holodeck often but enjoyed reading instead. When he did use the holodeck, he enjoyed developing relationships with characters in programs. He also enjoyed boxing in the holodeck, which he said helped him relax. ()
He occasionally took the time to embrace his artistic side, such as creations using colored sand while trapped on "New Earth" and carvings of Native American symbols. ()
===Spirituality===
When younger, Chakotay had little interest in the traditions of his tribe or in spirituality. However, he connected with the spirituality and traditions of his culture as an adult out of respect to his father, who was killed by the Cardassians while defending the planet his tribe lived on, a connection that grew because of his experiences on Voyager far from home. (On one away mission, he actually met the sky spirits his ancestors prayer to.) () He carried out rituals, like pakra (to commemorate the anniversary of his father's death) and vision quests, praying and using his medicine bundle. () He would seek guidance from his animal guide and used a medicine wheel for physical and spiritual healing. () He would pray for others and also acted as a spiritual guide and counsel to others. () He was noncommittal on the existence of an afterlife, stating that he accepted there were "things that can't be scanned with a tricorder". () He recognised that vision quests, while spiritual practices, were underlain by science. () He said that to understand what one experienced in a quest or similar ritual was a process that involved careful consideration of what the elements of the quest were symbolising. ()
===Foods ===
Chakotay was a vegetarian; one of his favorite meals was mushroom soup. () Some foods he hated were carrots and fried food (because it upset his stomach), and he refused to eat pudding because he thought it was slimy. () Neelix was aware of his dietary choices. During a trade mission to the Nar Shaddan in 2377, he did not press the delicacy of falah nectar on Chakotay because the beverage was made from a meat byproduct, even though it would have been a diplomatic gesture; Neelix convinced Harry Kim to try it instead. ()
Chakotay preferred to avoid alcoholic beverages when possible, saying he preferred to "stay in control". (). One of his favored beverages was Antarian cider that he kept a secret stash of hidden in the cargo bay 2. ()
If Seven of Nine's holographic recreation of him was true to life in this regard, Chakotay was an inexperienced cook with poor cooking skills, calling himself more of a "replicator man". ()
=== Anthropology and paleontology===
One of the many reasons he joined Starfleet was to pursue his interests in anthropology and paleontology. He was fascinated by 20th century Earth during Voyagers visit to its 1996 from 2373, and said that if they were trapped there, he might become an anthropologist. Once, he considered becoming a paleontologist as well. ()
While serving in Starfleet, he visited a tomb excavation on Ktaria VII. ()
In 2373, while examining the Distant Origin Theory, Chakotay suggested that the Voth might have evolved on an isolated continent on Earth and that natural disasters could have buried the evidence under water or rocks. ()
The depths of Chakotay's thrill for anthropology was perhaps revealed in 2375 when the telepathic pitcher plant tricked the Voyagers crew into its digestive tract by making them believe they were entering a wormhole home. As part of the deception, it made them believe they were going to get what they most wanted when they returned. Chakotay imagined he'd received a full pardon for his actions as Maquis – and a professorship of Anthropology at Starfleet Academy. ()
Chakotay was interested in the early history of space exploration, John Kelly being one of his childhood heroes. So when Voyager got the chance to actually find his ship in 2376, he was more than eager to salvage the craft when he'd found it intact. Too eager in fact – he injured himself, damaged the Flyer and endangered his crew in his attempts to claim the craft before leaving the graviton ellipse it was caught in. Seven of Nine had to beam aboard the Ares IV, to retrieve a component to fix the Flyer, and Chakotay tried desperately to get her to realize how special it was. As a result, Seven played several of Kelly's logs that were left active when she beamed aboard. He was able to use his skills and knowledge of paleontology to explore various other items caught in the anomaly, saying he could happily stay inside it for a longtime discovering things about the universe's history. ()
Later that year, he was very interested in a planet they discovered that moved at an accelerated rate compared to normal space-time. Despite Voyager being trapped in the planet's orbit and in danger, he still had a deployed probe take images as the civilizations developing below, saying it could be the greatest anthropological find of his career. At one point he commented that every second they missed they could be missing "whole civilizations", to which Torres replied "So? We'll catch the next one." ()
In 2378, Seven and Chakotay were trapped together again, this time on a world inhabited by the primitive "Ventu", who Chakotay was fascinated with. His interest in anthropology helped him to understand their culture, and he even learned many of the phrases in their sign language. ()
He told renowned Voth molecular paleontologist Forra Gegen he was a scientist too and spoke of years studying science alongside navigation and starships to Kar. ()
===Boxing===
Since his time at Starfleet Academy, Chakotay was a fan of boxing. While there, the legendary Boothby helped him train. On Voyager he occasionally ran a program on the holodeck where he would box a with Boothby's assistance. He also said that boxing helped him relax.
In fact, in 2375 while running this program an alien species that lived in chaotic space tried contacting him and used images of the boxing simulation in their communication. ()
He was also a fan of professional sumo wrestling, once getting into an argument about the 77th Emperor's Cup. ()
In 2376, while on shore leave on Norcadia Prime he came across a martial art called Tsunkatse on. He was quite a fan, discussing various fighters' statistics with other members of the crew, and made sure he was able to watch several of the matches live. Although The Doctor didn't approve of Tsunkatse (or boxing, for that matter), Chakotay insisted it was an excellent way to test a warrior's skills and instinct. ()
==Personal relationships==
Chakotay got along with most of the people he worked with and had many personal relationships among the crews of both the Val Jean and Voyager. On his Maquis ship, people were very informal, so he got to know his crew on a very personal level. He got the respect of the Voyager crew when Janeway put her trust in him by making him first officer and when he decided to re-embrace Starfleet principles. He forged a deep and meaningful friendship with his Captain, but never hesitated to speak up when he believed that she might be making an unwise move. He was also often the liaison between the crew and the captain, as people trusted him. In the beginning, Chakotay felt that some of his former Maquis crew members might be unfairly judged, so he always had a soft spot for them and did his best to stand up for their interests, especially when he felt that no one else was. 
While he was not the kind of person to hold a grudge, he also knew when to be tough and enforce the rules. On one occasion, when two of his former Maquis friends, Jarvin and Seska, suggested that they would support him if he wanted to mutiny against Captain Janeway, Chakotay told them point blank that if he ever heard them talk like that again, he would personally throw them in the brig. He also occasionally turned to rather unconventional non-Starfleet methods to discipline his former Maquis crew members who had a little more difficulty or were unwilling to adjust to Starfleet standards: on one occasion, when Kenneth Dalby disrespected Tuvok's orders and just walked out on him after he was specifically ordered to participate in special training, Chakotay decided to teach him a lesson "the Maquis way": he walked into the mess hall and knocking Dalby out of his chair, saying that this was the way the Maquis handled situations like this and that he could continue to do it "the Maquis way" until everyone got it. Dalby and other troublemakers got the point and became more cooperative. Situations like this were rare, however, and through his journey aboard Voyager Chakotay was able to remain on good terms with almost everybody. ()
=== Friends ===
====Kathryn Janeway====
From early on in their time on Voyager Chakotay and Kathryn Janeway forged and maintained a relationship based on deep respect and admiration for the other. In fact, Janeway once remarked that while just a few years ago she did not even know his name, now she could not imagine a day without him. Chakotay would reassure Janeway when needed and he recognised Janeway as an excellent captain who could face the biggest of challenges. The mutual respect they had for each other was never lost even when they disagreed quite vehemently over command decisions, although their trust for each other was shaken a few times and had to be rebuilt. (, )
They got off on a shaky start when they were first trapped in the Delta Quadrant and Chakotay had reservations about destroying the Caretaker's array that was going to leave Voyager and his own Maquis stranded in an unknown part of the galaxy. For the sake of cooperation and survival of both of their crews he submitted to Janeway's authority. ()
They also shared a certain chemistry that eventually became evident to both of them while they were trapped on a planet in Vidiian space they called "New Earth." The two were infected with a virus that trapped them on the planet, and while Janeway tried to find a cure – as Voyager had continued on its mission – Chakotay preferred to make the planet their home. The two formed a familiarity during their isolation and Janeway invited Chakotay to call her by her first name, Kathryn. After a long day repairing damages caused by a plasma storm, Janeway complained about an ache in her shoulders. Chakotay offered to give her a massage, which she enjoyed until she realized it probably wasn't appropriate for them to become this intimate. She couldn't sleep that night, and when she attempted to "define parameters" about their relationship, Chakotay reassured his allegiance to her whatever their form their relationship would take. In this intimate moment, Chakotay said that he had been a discontented and angry person before he met Janeway. Through a story, he called her "brave and beautiful and very wise" and said he would do "whatever he could to make her burden lighter", putting her needs first. By doing this, he said, he had found peace. After their conversation they held hands across the table. After a cure for their illness was found and they were finally rescued, they silently agreed that certain things were better left behind on the planet, and resumed their respectful and cordial relationship, although their chemistry was still present in the background from time to time. As Chakotay put it at one point, there were "some barriers [they] never cross[ed]". Chakotay continued to call her by her first name, a unique intimacy that no one else on the crew was ever invited to do. () 
While accepting and respecting Janeway as his captain, Chakotay never hesitated to speak up and assert himself when he felt that the situation required it or when Janeway was making questionable command decisions. Months into Voyagers journey and after constant attacks by the Kazon, Chakotay urged Janeway to reconsider her position with regard to the Kazon and think more like the Maquis. He felt that Starfleet regulations were too rigid for them to survive their journey through that part of space. He suggested they seek alliances with other sects of the Kazon. Hesitant at first Janeway agreed to reconsider her position. () He also did not agree with her decision to bring a Borg drone she had disconnected from the Collective along on their journey through the Delta Quadrant, believing it nearly impossible that Seven of Nine could ever be anything but an automaton. () 
On another occasion he refused to let her go off alone on a dangerous mission to destroy the Omega molecule after it had been detected by long range sensors. He said to her, "You're asking me to abandon my captain and closest friend without even telling me why". Janeway asked that he trust her, but Chakotay remained adamant, telling her that the mission would succeed if they worked together, not if she just went off on a suicide mission by herself. He emphasized that they were a team and as such she could count on them for support, even if Starfleet orders said otherwise. () In 2375, he staged yet another intervention when Janeway once again insisted on taking matters into her own hand and going off on a one-way mission to save her crew: they had entered a vast region of space with no stars or systems, and their only way out of the void was through a spatial vortex. The Malon used the vortex to dump their poisonous antimatter waste into the void, which in turn poisoned the species indigenous to that void. Reasoning with the Malon failed and Janeway soon realized that the vortex had to be destroyed so the Malon could not return to it; however, this time she was not willing to sacrifice her crew once again to save another species, like she had done with the Ocampa and the Caretaker's array. Therefore, she decided to stay behind after Voyager passed through the vortex, so she could destroy it. Chakotay did not want to allow her to make such a sacrifice and, working with the crew, he made sure they all refused to carry out her orders. She was outwardly upset at this rank insubordination, but it was evident that she was actually touched by their action. ()
A similar incident happened towards the end of Voyagers sixth year in the Delta Quadrant, when Janeway, in response to a request for help against the Borg, planned a solo mission to a Borg vessel to introduce a nanovirus into the Collective. Prior to Janeway revealing she'd be going on her own, Chakotay had given his support to her. However, believing this element of the plan to be too risky, Chakotay insisted Janeway take Tuvok and Torres with her. When Janeway said she thought she had his unconditional support this time, Chakotay replied, "This is the best I can do" and indicated he would take measures to stop her from going alone, if he had to. Janeway agreed to to take Tuvok and Torres on the mission.
As they approached the Borg vessel and Janeway went to join the away team, perhaps realising the seriousness of this mission, she reached out a hand to Chakotay, who held it as they both stood and Janeway gave command of the bridge over to him. ()
One of the most serious conflicts between them occurred during the encounter with the in 2376: the Equinox, which was commanded by Starfleet Captain Rudolph Ransom, had been using sentient nucleogenic lifeforms as fuel for his ship. When Janeway found out about Ransom's actions which violated every Starfleet directive and code of moral conduct, she was disgusted and furious. When the Equinox tried to escape, Janeway, who felt betrayed and enraged about Ransom's atrocious actions, began a relentless hunt, even going so far as to compromise the safety of the ship and its crew to get to Ransom. Chakotay confronted her about the issue, accusing her of having tried to satisfy a personal vendetta at the cost of the ship. Janeway remained relentless, however, and told him that she wasn't going to stand by and let Ransom torture and murder innocent lifeforms just so he could get home a little sooner. Chakotay tried to get through to her but to no avail. When she resorted to torture of one of Ransom's crewmembers in exchange for information, he warned her that he wouldn't let her cross that line again. Upon hearing this, Janeway, blinded by her desire to bring Ransom to justice, relieved him of duty. 
After Ransom had a change of heart and surrendered to Voyager, Janeway returned to her senses. In a silent moment, she told Chakotay that he may have had good reason to stage a little mutiny of his own. Chakotay admitted that the thought had occurred to him, but that it would have been "crossing the line." This struck a chord with the captain who realized how close her recent actions had come to being no better than that of the Equinox and Captain Ransom. ()
Even though Chakotay considered Janeway to be one of his closest friends, he also found her to be sometimes an unreasonable person who did not know when to step back. During another incident three years earlier involving the Borg and Janeway's decision to strike a deal with them in exchange for safe passage through their space, Chakotay told her point blank that what she was proposing was foolish and too great a risk. Using the parable of the scorpion, he tried to explain to her that the mission she was planning to embark on was doomed to fail as the Borg were not the kind one could strike equitable deals with. He also believed Janeway's decision to be selfish as she was willing to supply the Borg with means to assimilate yet another species just so she and her crew could get home faster. When Janeway asked him to trust her he remained steadfast with his belief, accusing her of being blinded by her desire to go back home no matter the cost. After a lot of arguing that was not going anywhere, however, both realized that in order for the mission to be successful, they had to set their differences in opinion aside and work together. Chakotay's objections ended up inspiring a backup plan between the two, in case the Borg turned on them; this ended up saving the crew. ()
According to Captain Janeway's mimetic duplicate, Chakotay was a "friend who wasn't afraid to let me know when I am wrong." Their working relationship was perhaps summed up informally by Janeway from an alternative future who, visiting the grave of Chakotay in her timeline, said, "Any final words of advice for your old captain? Wait, don't tell me. I'm being impulsive. I haven't considered all the consequences. It's too risky. Thanks for the input, but I've got to do what I think is right". From Chakotay's perspective, he came to recognised that it was his duty to advise Janeway but that she would always make the final decision. ()
Chakotay's relationship with Kathryn Janeway wasn't always controversial. Early during their voyage home, he shared with her some of his spiritual rituals, such as how to embark on a vision quest and talk to her "animal guide". He also showed and shared with her his private medicine bundle. They often had weekly dinners together and once went on a moonlight sail on Lake George. He was also the first person she confided the end of her relationship with her former fiancé Mark Johnson to, who in 2374 revealed in a letter that after believing her lost, he moved on and married another woman. They remained great friends throughout and she even lent Chakotay a copy of Dante's Inferno given to her by Mark, which she'd never lent to anyone. They were supportive of each other and Chakotay was happy to see her have some fun when she in 2376 had developed an interest in one of the characters of the Fair Haven program created by Tom Paris, encouraging her he enjoy it when she was embarrassed about having feelings towards a hologram. () When a Janeway from a passed timeline, evidently struck by him, asked him about the closeness of their relationship in the future, he simply replied that there were some barriers they never crossed. ()
Her love for Chakotay was one of the reasons Admiral Janeway risked time traveling back to Voyager and sacrificed herself to help the ship get home quicker. She desperately wanted to avoid Seven of Nine's death, which happened during that Janeway's 23-year journey home, and the trauma it caused to Chakotay, who was married to Seven by that point. ()
====B'Elanna Torres====
B'Elanna Torres was Chakotay's engineer, and unofficial first officer aboard the Val Jean, and the two shared a close friendship as well as working relationship for years. Despite their occasional differences, Chakotay was the one she trusted the most and probably also the only who truly understood her nature and inner struggle; she often returned to him for guidance. 
With a fiery temper mostly from her Klingon side, Torres was the first to speak up that it wasn't Captain Janeway's right to destroy the Caretaker's array and thus get them all stranded in the Delta Quadrant. Speaking as her commanding officer, however, Chakotay made it clear who the captain was. From then on, Chakotay asked his entire crew to respect Janeway as their leader and embrace the Starfleet way. Initially, the most hesitant and resistant person to do this was Torres. ()
Voyagers violent hurtle into the Delta Quadrant cost them the lives of many of their crew members, leaving key positions open that needed to be filled urgently. One of those positions was that of chief engineer which Chakotay championed for Torres to get, even though Joe Carey was next in line. Chakotay, knowing that Torres was the better engineer, insisted that Janeway consider her for the position. Although Janeway thought it was a long shot, as she saw Torres as brash and incapable of exhibiting the kind of professionalism required from a command officer, he continued standing up for her, insisting that if she only gave her a chance, Torres wouldn't disappoint her. He also told Torres that she would have to start treating people better if she wanted to get ahead on the ship and make it. Even though Torres put up a fight, she was thankful that Chakotay still believed in her; after proving herself to Janeway, she got the job. ()
Torres didn't instantly become a model Starfleet officer though, and it took her some time and a few lessons to turn her life around and fully embrace the Starfleet crew. () Whenever she needed someone to turn to when she was going through a rough patch in her life over, she'd go to Chakotay. They often relied on each other when they needed their emotional compass checked and when they needed to put things into perspective, but Chakotay was never hesitant to tell her like it is when she behaved stubbornly or out of line. He also never played favorites with her due to the past they shared, even though it was sometimes difficult for him to separate the strong friendship they had shared over the years from his standpoint as the first officer. ()
As friends, they did spend time together engaging in various activities; the two occasionally played hoverball together on the holodeck, though he wasn't very good. On one occasion, she was beating him 19 to 7, but he claimed he was just lulling her into a false sense of security. Chakotay had also helped her find her animal guide and he prayed with her when they both believed they were going to die. Even though they had always shared a friendship and never crossed the line into romance, Torres felt a hidden attraction toward Chakotay. This was revealed when the Botha manipulated the crew and induced disturbing hallucinations in them and Torres was carried away by a passionate hallucination involving Chakotay. She never acted on her feelings for him, however, and was able to move on. ()
When Chakotay once left Voyager – without authorization – in order to pursue Seska, it was Torres who pleaded with a rather upset Captain Janeway to try to understand Chakotay's struggle and the humiliation he faced after Seska's betrayal, asking her not to lose faith in him as her first officer. Janeway remarked that Chakotay was quite lucky to have someone care about him as much as Torres did. 
Around 2374, Chakotay received word from one of his Maquis friends back home that the insurrection was over, and that the Maquis had all been wiped out by the Cardassians and their ally from the Gamma Quadrant. The news both saddened and angered Torres, who realized that everything she had known and fought for back home was gone. Through the course of the year, she regularly went to the holodeck and played the most dangerous programs she could find with the safety protocols offline. This eventually impaired her ability to work, and although Janeway confined her to her quarters and took away her holodeck privileges, Chakotay took the time to find out what was really bothering her. He even took her down to the holodeck, leading her to believe they'd play a simple program – and instead, he forced her into a program where she was re-enacting the massacre of the Maquis. He forced her to face her inner demons and come to terms with the fact that they both wished they could have been there to help their friends fight the good fight, but that because they hadn't been there, it didn't mean that they did not deserve to live and move on with their own lives. ()
When in 2377 Torres found out she was pregnant, he came up to her and jokingly asked, "Have you checked the warp core for radiation leaks today? … You have a certain glow about you." She immediately knew someone had told him. Chakotay would have liked to be the child's godfather, and even suggested several names – such as Taya, the feminine form of Chakotay – but recognised, perhaps more than others, that parental advice and suggestions from others could become irritating to the parents and knew when to step back, which Torres appreciated in him. In the end, Torres decided not to choose Chakotay to be the godfather, in part because she believed he didn't really know about raising children. ()
The mimetic duplicate of Chakotay walked Torres down the aisle and gave her away to Tom Paris during their wedding aboard the duplicate Voyager in 2375. ()
====Tom Paris====
Chakotay knew Tom Paris from a time when Paris had joined the Maquis after his disgraceful discharge from Starfleet. He didn't like Paris because unlike himself who had joined the Maquis on moral grounds, he saw in Paris nothing more than a mercenary, willing to fight for anyone willing to pay his bar bills. Needless to say, he was not too happy to see him on Captain Janeway's bridge after they were stranded in the Delta Quadrant. 
They eventually came face to face, after the Caretaker had released them to their ships, and Chakotay was forced to cooperate with Janeway. Although Chakotay was particularly angry at Paris, possibly added to by the fact he'd just found out that Tuvok was a spy, Janeway asked Chakotay to grant Paris the same respect he expected her to show his crew. The two were able to come to terms enough to go down to the planet together, and when Chakotay broke his leg trying to escape, Paris went back to save him. When Chakotay told him to leave, Paris snarked that if he saved Chakotay's life, it would belong to him. The two eventually made it out safely, and Chakotay joked to the captain when they returned that his life belonged to Paris and volunteered to be his "personal bodyguard," against possible hostility from the former Maquis crew. ()
In 2372, Paris pretended to harbor animosity towards an unknowing Chakotay in order to expose a traitor on board Voyager. During this time, he regularly showed up late to his duty shift, set up a gambling operation which Chakotay broke up and he eventually pushed Chakotay to the floor of the bridge when called on his unacceptable behavior. He also loudly expressed his negative opinion on Chakotay's role as first officer in Voyagers mess hall to many crewmembers. The two later set aside their differences when Chakotay finally found out about Paris' true intentions, and in an interview with Neelix, Paris particularly apologized for giving Chakotay such a hard time as part of his role. From that point onward, they buried their hatchet for the last time and finally got over their past animosities and hard feelings for one another. () Chakotay, for his part, frequently addressed Paris by his first name, suggesting a certain level of affection, and by their seventh year together appreciated Paris', saying "we love having him around". ()
====Tuvok====
Chakotay and Tuvok served together on the Val Jean, where Tuvok was posing as an undercover agent for Starfleet in order to infiltrate Chakotay's cell. After they had been stranded in the Delta Quadrant by the Caretaker's array, Tuvok's real identity was soon revealed. This angered Chakotay who felt fooled and betrayed by Tuvok. However, as the nature of their situation required, they maintained a cordial relationship when they were forced to cooperate and work together aboard Voyager. ()
When Captain Janeway picked Chakotay as her first officer over Tuvok, Tuvok was disappointed but respected her decision. Tensions between the two still occasionally arose, especially when Tuvok kept reciting Starfleet protocols and procedures to Chakotay who sometimes had his own way of doing things. When B'Elanna Torres had punched Lieutenant Carey in the nose, and this accident landed him (Carey) in sickbay, Tuvok insisted on having her put in the brig, pointing out that striking a fellow officer was considered a court martial offense. Chakotay, understanding Torres' ways and that she could succeed if given a chance, asked Tuvok to drop the matter as he would discipline her in another manner. () 
They also occasionally disagreed over command decisions such as the time when Voyager encountered an inversion field which had twisted and distorted the ship's hull. Tuvok suggested accessing the navigational array and from there engaging thrusters. Chakotay, however, decided to follow Torres' suggestion. This lead Tuvok to second-guess Chakotay's decision, which in turn irritated Chakotay who reminded him that he was in command. When it turned out that Tuvok's suggestion would indeed have been the wiser choice, Chakotay admitted that while he sometimes found Tuvok arrogant and irritating, he nonetheless believed him to be "one hell of an officer". Tuvok responded that while he in fact hadn't always been particularly partial to his methods either, he had always respected Captain Janeway's decisions, even though her decision to make Chakotay first officer put him in a position he was unaccustomed to. Tuvok apologized if that had ever caused him to make things more difficult for Chakotay, an apology Chakotay graciously accepted. () 
Throughout their journey back home, their relationship gradually softened, and both came to greatly appreciate and respect the other. On one occasion, when a former Maquis crew member directly disobeyed Tuvok's orders, Chakotay even went so far as to personally set him straight, making sure he understood whose orders he needed to respect on the ship and that disobedience of those the Maquis did not personally approve of would have its consequences. ()
When Voyager was traversing what they dubbed "" in 2375, Janeway fell into a deep, guilt-based depression over the ship being trapped in the Delta Quadrant due to her decisions. Worried, Chakotay relied on Tuvok's knowledge of her past and her psyche to predict that she would likely resort to self-sacrifice to protect the crew. When asked by Chakotay, Tuvok pledged his support in preventing any such outcome. ()
=== Romance===
====Seska====
 
Seska and Chakotay were not only together in the Maquis, but they were also romantically involved sometime in the past, although they had eventually decided not to pursue their relationship any further. A certain attraction between them still existed, however, and when Chakotay once reminded Seska of their decision to not be together anymore, she laughed it off, joking that stranded in the Delta Quadrant, he didn't have all that many options. 
Despite being hesitant to pursue a romantic relationship with her, Chakotay nonetheless remained very protective of Seska and when she was accused of sabotage and collaboration with the Kazon, he was the only one on her side until, much to his disappointment, evidence proved that she was indeed betraying them. She not only had collaborated with the Kazon, but it turned out that she was in fact a Cardassian spy who had her physique surgically altered to look Bajoran in order to infiltrate Chakotay's Maquis cell. She insisted, however, that she had only one agenda with Chakotay which wasn't all that secret. 
Shortly after she was exposed and before her departure from Voyager, she expressed her deep disappointment in Chakotay who had decided to take on "mighty Starfleet principles", which she believed to be responsible for their perilous situation. She wondered how she could ever have loved him. () 
After this betrayal by Seska, Chakotay felt a great sense of shame and disappointment, because she had not only taken advantage of his trust and care for her, but also because after everything he had done for her, she publicly humiliated him by turning out to have been a Cardassian spy who now had, once again, turned her back on him by defecting to the enemy. 
After Seska fled Voyager, she joined Maje Culluh of the Kazon-Nistrim, constantly plotting new ways to capture Voyager. In one instance, she lured Chakotay into a trap in which he was caught and tortured by Culluh and his men unsuccessfully for information about Voyager. She used that opportunity to artificially inseminate herself and eventually gave birth to a baby boy she claimed to be Chakotay's son. 
Unable to abandon his child, Chakotay – as soon as he found out – pursued her. It turned out to be a trap once again, and Chakotay's pursuit led to the capture of Voyager by the Nistrim and to the crew being marooned on a desolate planet. 
The Doctor, who had stayed aboard Voyager when the Nistrim took over, examined the child and much to Seska's surprise revealed that the baby was half Kazon and thus not Chakotay's son. 
A rescue attempt led by Tom Paris lead to the Nistrim being forced to abandon Voyager. it was during Paris' rescue attempt when Seska received a high dose of electric charge at one of the consoles and shortly after died with her baby in arm. Culluh took the baby with him when leaving Voyager, leaving her remains behind – which Chakotay later found when retaking the ship. ()
In 2371, Seska had found Tuvok's Insurrection Alpha holonovel training program depicting a Maquis mutiny and reprogrammed it with the goal of trapping Tuvok and anyone with him inside the program the next time he tried editing the narrative parameters file, and with the safety protocols turned off. The novel portrayed a holo Chakotay programmed to be strongly enamored by Seska, and the two were enthusiastically living out their old wild Maquis ways. ()
====Kellin====
, a Ramuran, who came from a closed society, fell in love with Chakotay on one of her missions to retrieve and bring back someone who had decided to leave their society. The Ramuran's biology was such that those whom they met couldn't hold their memories of contact with the Ramurans for more than a few hours. Similarly, Ramurans who escaped also had their memories of the new species they encountered wiped out. Kellin explained that she had visited Voyager previously and that she and Chakotay had fallen in love. Chakotay was taken aback by the things Kellin said and it took him a while to fall in love with her again. 
Shortly after Kellin's return, the Ramurans pursued her and an agent beamed aboard to take her back; he hit her with a neurolytic emitter and wiped out her knowledge of Chakotay. Chakotay tried hard to get her to remember him and what they felt for each other, but with Kellin's memory of Chakotay and their feelings for one another wiped out, Kellin just wanted to return to her world and was not interested in pursuing a romance with Chakotay. As she left, Chakotay – knowing that he would soon forget about her and that all electronic records would be wiped clean as well by the Ramurans, began handwriting down his memories of her visit, so they wouldn't be forgotten. ()
====Valerie Archer====
Valerie Archer and Chakotay (calling himself Jason Hayek) met while Chakotay was on a reconnaissance away mission investigating a recreation of Starfleet Command and Starfleet Academy constructed on a space station in the Delta Quadrant. At first unbeknownst to Chakotay, Archer was one of Species 8472, genetically modified to look Human. Chakotay's initial interactions with Archer, while flirtatious, were solely for the purposes of finding out information, while Archer's were for the purpose of practicing acting like a Human (Species 8472 were running the recreation as a training facility to prepare trainees to infiltrate Starfleet on reconnaissance missions). When they met a second time, for a date suggested by Archer, both were using the interaction for espionage (Archer had been informed by her superior that Chakotay might be a Human and had been charged with investigating him). However, by the end of the date, when Archer initiated a kiss (ostensibly as part of her training to learn more about the Human species), Chakotay, initially resistant, kissed Archer passionately. The kiss was a ploy by Archer to get a genetic sample from Chakotay to test what species he was. Having informed her superior that his suspicions were correct, Chakotay was caught before he managed to leave the space station. During interrogation and a procedure to extract more of Chakotay's DNA to improve Species 8472's genetically engineered disguises, Chakotay managed to further engage Archer on an intellectual and empathetic level. While their relationship had initially been based on suspicion and utility, a genuine romantic and respectful connection developed between the two during their times together. Their evident mutual respect and trust was persuasive to their superiors during the subsequent diplomatic engagement between Voyager and Species 8472 to try to avoid conflict. When the two sides had reached an agreement, Chakotay and Archer met again and expressed their appreciation for each other, indicating how they would have liked to be able to spend more time with each other. Archer said it was a shame their two species were so different, otherwise she would have asked him for a second date. Chakotay said Archer had made a "terrific Human" and that he would like Archer to give him a tour of her relm (i.e., fluidic space) in the future; Archer replied that she would like that. Before they parted, Archer initiated another kiss, which they both enjoyed. ()
====Seven of Nine====
Seven of Nine and Chakotay got off to a rough start; he initially saw in her a mere drone that was not to be trusted. He made it clear to Captain Janeway that he did not think it was a good idea to take her along on their journey, stating that trying to bring her back to Humanity might be impossible as her Borg part might always cause complications and haunt her. He also disliked Seven's adversarial and insubordinate attitude toward Captain Janeway in particular and ship regulations in general and he once voiced his concern of allowing her to be the sole person in charge of Voyager when it was passing through a dangerous Mutara class nebula. () 
As their journey progressed and as the crew began slowly warming up to her, Chakotay also began seeing in Seven a valuable crew member. His impression of her changed and he no longer believed that she could not make it as Human. He told Captain Janeway once that when she first came aboard, he did not think that she would last a day, much less a year. He was glad that Janeway had proven him wrong in that regard. () 
On one occasion he encouraged her to take on three former child drones from her former collective by having their neural implants removed so they could live as individuals. () When in 2376 she asked to be relieved as the children's guardian – mainly because she couldn't get them to obey her rather rigid schedule that allotted specific times for "fun" – Chakotay denied her request, stating that she treated the children as if they were still on a Borg cube, making them do the same things at the same times and not allowing them to express their individuality. He encouraged her to grant them some leeway and spontaneity so they could develop as individuals. ()
In 2378, while trying to explore different aspects of her Humanity such as social activities and intimate relations, Seven began playing with the possibility of a romantic relationship with Chakotay. She simulated a few dates with her new love interest on the holodeck. ()
When Seven's cortical node shut down during the simulations she was running, mainly because of a certain level of emotional stimulation she had experienced, she decided to terminate her experimentation with dating and the strong emotions that followed it. It turned out that the shutting down of her cortical node was a fail-safe mechanism to deactivate drones who started to regain their emotions. Even though The Doctor offered to help her to function normally again through several operations, Seven refused, stating that all those holographic fantasies were an inefficient use of her time. She was also quite embarrassed that The Doctor had found out about her fantasies with Chakotay but knew that he would keep that information confidential. ()
However, The Doctor did not give up and several months later was able to devise a safe method of removing her implants in one surgical procedure. This gave Seven the freedom to experience emotions without the feared repercussions and she finally began pursuing a relationship with Chakotay. On one date, she prepared a picnic in cargo bay 2 for them, complete with wine, which the Chakotay described as "perfection." Later, they had a private dinner in Chakotay's quarters. Seven transported in, saying she didn't think it would be seen as appropriate carrying flowers to the first officer's quarters. To avoid the uncomfortable anticipation of the first kiss, Seven figured it would be best if she got it over with and kissed him. When Chakotay asked about the second kiss, she replied she'd have to check her research – but the two continued passionately, until being called to the bridge moments later. ()
In an alternate timeline, Admiral Janeway revealed to her that Chakotay and Seven got married in that timeline, and that she died while he remained heartbroken. Upon hearing this, Seven tried to break off the relationship with Chakotay in order to save both of them from a lot of heartache, but Chakotay refused to let her end it based on what he believed to be mere speculation and they decided to continue their romance despite what they had heard. ()
==Alternate Chakotays==
===Biomimetic duplicate ===
In 2374, the Voyager, while dangerously low on deuterium as fuel, landed on a Demon Class planet rich in deuterium sources. The planet was filled with silver fluid with mimetic properties. The Silver Blood sampled the crew's DNA and created duplicates with identical memories and personalities but with the ability to survive on the planet. The silver blood would not let Voyager leave unless it could duplicate the rest of Voyagers crew to populate the planet. Captain Janeway, understanding that this was their only way out, allowed the "silver blood" to duplicate the crew. In 2375, this duplicate ship – unaware that it was a facsimile of the original Voyager crew – began suddenly dying one by one due to warp drive radiation. Upon finding out their true identities, "Chakotay" argued with "Janeway", who wanted to carry on towards Earth, that they should return to their real home, the Demon class planet, or the entire crew would die. "Janeway" refused but was convinced when "Chakotay" died from the raditaion. In her impromptu eulogy informing the crew of his death, "Janeway" called "Chakotay" a "friend who wasn't afraid to let me know when I am wrong". Unfortunately, everyone died before the ship could reach home. ()
===Holograms ===
Chakotay was holographically duplicated on a number of occasions:
*Recreations of crew members from Voyager and the Jupiter Station Holoprogramming Center were seen by The Doctor during a holographic malfunction in 2371. This simulation, or daydream, included Chakotay. ()
*The entire crew of Voyager was recreated by Tuvok from his Insurrection Alpha program, including Chakotay, who was depicted as the leader of the Maquis mutiny. ()
*The Kyrian Museum of Heritage in the 31st century used the program The Voyager Encounter to detail their encounter with the as an aid to a history lesson. In that recreation, Chakotay (whose name in the simulation was pronounced differently) was depicted as a cold-blooded killer working for an equally cold-blooded captain, who had ordered the genocide of millions of people. His tattoo was shown to be a lot bigger, covering half his face. ()
*In 2374, The Doctor recreated the crew of Voyager, including Chakotay, in order to help Seven of Nine improve her social skills. ()
*Lt. Barclay's recreated most of the crew of USS Voyager at the Communications Research Center on Earth for the Pathfinder Project in 2376. The Maquis crew members, including Chakotay, were not wearing Starfleet uniforms. ()
*In 2378, Seven recreated the crew of Voyager to perfect her social skills, including Chakotay, who is her romantic interest and encouraged her to explore her Humanity through music and their relationship. He is sad when Seven ends their relationship, pleading with her to reconsider. This Chakotay can't cook, calling himself a more of a "replicator man". ()
*The Doctor's holonovel Photons Be Free was set aboard the and crewed by characters based on the crew of USS Voyager, albeit the names were changed to protect the innocent. The character of Katanay was based on Chakotay. ()
*The Doctor was forced to impersonate members of Voyagers crew during a crisis in 2378. One was Chakotay. ()
===Alternate realities and timelines===
In another timeline, Chakotay and Harry Kim flew the Delta Flyer to Earth after Voyager was destroyed due to a mistake of Kim's. Fifteen years later, as fugitives, they found Voyager and "fixed" history. ()
Another separate timeline was created when Captain Braxton, from the 29th century, placed a temporal disruptor aboard Voyager, creating several temporal distortions. At one point while Chakotay was giving a damage report to Captain Janeway, he passed through a temporal distortion, and appeared to echo – both his voice, and his appearance. ()
In an alternate timeline, Chakotay married Seven of Nine, who later died on an away mission. He himself died in 2394, the same year as Voyagers return. According to Admiral Janeway, shortly after Voyagers return Chakotay died from grief over Seven's death. He had a grave marker at a cemetery on Earth. ()
In another alternate timeline experienced by Kes, Chakotay was captain of the USS Voyager after Captain Janeway and B'Elanna Torres were killed by a chroniton torpedo in a Krenim attack in 2374. ()
==Key dates==
*2329: Year of Birth
* 2344: Enters Starfleet Academy
*2348: Graduates from Starfleet Academy
*2368: 
**Resigns from Starfleet
**Joins the Maquis
*2368 – 2371: Member of the Maquis
*2371 – 2378: First officer of the USS Voyager
* Between 2378 and 2383:
**Promoted to Captain
** Given command of the USS Protostar
*Late 25th century: Imprisoned on Solum
== Memorable quotes==
"I have no intention of being your token Maquis officer!"
: - Chakotay ()
"We talk to animals."
: - Chakotay ()
"You were working for her, Seska was working for them, was anyone on that ship working for me?"
:- Chakotay, to Tuvok ()
"Trapped on a barren planet and you're stuck with the only Indian in the universe who can't start a fire by rubbing two sticks together!"
: - Chakotay ()
"Is there something on your mind?"
"Yes, but you're not going to like it."
"That's never stopped you before." 
: - Janeway and Chakotay ()
"I guess you never assimilated any Indian scouts."
: - Chakotay to Seven of Nine after she had missed a set of footprints giving a clue to the direction of their missing crewmates ()
"Maybe you can just flip some Borg switch and shut down your emotions, but I can't!"
: - Chakotay, to Seven of Nine ()
"Mayday! Mayday! The Protostar sustained heavy damage after passing through a temporal anomaly."
"Captain, send out the warning. We're being boarded."
: - Chakotay and Hologram Janeway as the Protostar is attacked ()
"Mayday. Mayday. It's day 72 since the Vau N'Akat captured the Protostar. They're planning to launch it back through the wormhole with a weapon aboard. Half my crew's gone, but I'm trying to hang on."
: - Chakotay's second distress call broadcast through the wormhole that Hologram Janeway opened ()
==Appendices==
===Appearances===
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===Background information ===
Chakotay was played by Robert Beltran during the course of Star Trek: Voyager. 
In , a younger Chakotay was played by Douglas Spain. In , he was briefly "portrayed" by Kate Mulgrew, Roxann Biggs-Dawson, Ethan Phillips, Garrett Wang, and Brian Markinson while possessing the bodies of their respective characters.
Chakotay was the first person to be seen in s series premiere, . In fact, the Native American character that became Chakotay was one of the first characters devised for Star Trek: Voyager. It was inspired by the positive influence that the character of Uhura has had on African Americans. Commented Executive Producer Jeri Taylor, "It seemed to us [meaning herself, Rick Berman and Michael Piller] that Native Americans needed that same kind of role model and that same kind of boost… the future looks good, you have purpose, you have worth, you have value, you will be leaders, you will be powerful. That was one character choice we had early on." (A Vision of the Future - Star Trek: Voyager, p. 174)
The as-yet-unnamed Native American was briefly mentioned in a set of handwritten notes that Taylor dated , and the character was outlined on , by which point his occupation as first officer for the new series (the similarly not-yet-named Star Trek: Voyager) had been decided upon. The outline read, "A Human native American male, 'Queegquog' person who has renounced Earth and lives as an expatriate on another planet. A mystical, mysterious man with whom the Captain has some prior connection, not explained." (A Vision of the Future - Star Trek: Voyager, pp. 175 & 176) On or by , the producers decided that, due to the character's allegiance to the captain, he would not be a likely candidate for wanting, in conflict with her, to settle for being stranded from Earth in the unexplored space that served as the series' setting. It was also decided that it would be "his people," rather than himself, who had renounced Earth and were living as expatriates on another planet. "This man has made another choice – to re-enter the world of Starfleet," explained notes dated 17 August, which also replaced the word "mystical" with "complex". (A Vision of the Future - Star Trek: Voyager, pp. 188-189)
To find out more about the character's Native American background, the producers enlisted the assistance of Jamake Highwater. (A Vision of the Future - Star Trek: Voyager, p. 199) Around , he forwarded the producers seven pages of research suggestions concerning Chakotay's background, though one point that remained undecided was the character's tribal ancestry. (A Vision of the Future - Star Trek: Voyager, p. 206) The fact that this had not been identified was noted in the first draft of the series writers' bible, which also named the character "Chakatoy". (A Vision of the Future - Star Trek: Voyager, p. 208) Ultimately his introduction in the premiere's script simply described him as "an intense Native American man in his late thirties" with "a tattooed face." 
The episode , which was written and aired well into Voyagers production phase, the lieutenant commander to whom Ro Laren refers as her instructor at Advanced Tactical Training in 2369/2370, and who joined the Maquis, was intended as a reference to Chakotay. As was the Native American connection made in that epsiode, and previously in (and ). (} 
Indeed, these original intentions about Chakotay were included in Ro Laren's biography at StarTrek.com but were ultimately nixed onscreen through contradictory information revealed in the Voyager fifth season episode . Here, Chakotay stated that he resigned his commission on , 2368, whereas according to his StarTrek.com biography, he resigned his commission in 2370.
Chakotay, as of PRO: "Cracked Mirror", is one of only four characters in Star Trek to meet their mirror universe counterpart face-to-face on screen. The others being Kira Nerys, Paul Stamets and Ash Tyler. Captain Jonathan Archer does appear in with , but only as a figment of the mirror Archer's imagination. 
====Rank====
Although Chakotay was invariably referred to as "commander" during the run of the series, his character wore what was indicated in reference materials to be the provisional officer rank insignia of a lieutenant commander (two solid stripes, one hollow stripe), a rank shared with his predecessor, Lt. Cmdr. Cavit. () While remaining true to production intentions from "Preemptive Strike", this was apparently a costuming error that continued throughout the course of all seven seasons.
While it has been shown to be generally accepted in Star Trek to refer to officers by the higher ranking component of their actual rank, as indicated with both Tom Paris and B'Elanna Torres being credited as "lieutenant", while in actuality being lieutenants junior grade, the same practice was not likely the case for Chakotay, who was otherwise identified as "Commander Chakotay" in the opening credits of virtually every episode from the first three seasons.
On Chakotay's choice to wear the provisional rank insignia (having resigned) versus being given standard commission like Tom Paris (who was discharged), , suggested that "while Chakotay would be entitled to a full commission, he chose to wear the same rank insignia as the rest of the Maquis, to show where his loyalties lay."
Aside from being initially addressed as "Commander Chakotay" in , even before joining the crew of Voyager, at least two other instances formally referred to him as a full "commander". The first instance appeared on the crew manifest shown in , while the second was referenced in , where his name, rank, serial number, position, and assignment were collectively revealed by .
===Character Bible description===
The First Officer is a complex – some would say difficult – man. His background is unique: he spans two cultures, one foot in each, belonging to both and yet to neither. In the twenty-second century, a group of Indian traditionalists became dissatisfied with the "homogenization" of Humans that was occurring on Earth. Strongly motivated to preserve their cultural identity, they relocated to a remote planet near what has now become known as the Demilitarized Zone.
Chakotay is a member of that Indian nation, but was always what his people call a "contrary;" he had a mind of his own, an individualistic rather than communal way of thinking. Though proud of his heritage and his traditions, he was not satisfied to ignore the galaxy around him – a galaxy teeming with diverse life-forms and amazing technology. He broke from his people, educated himself in the ways of the twenty-fourth century, and attended Starfleet Academy.
But he was "contrary" at the Academy, also, and found he had difficulty adhering to the rigid codes and rules. He was commissioned and posted to the Merrimac just after the end of the Cardassian wars. When he learned that his people were becoming victims of attack by Cardassians, he left Starfleet to defend them, joining the then-infant group, Maquis. Chakotay never gave up his practice of traditional rituals, and he preserves them aboard Voyager. In his quarters is an Indian altar and other traditional ritual items. One wall contains a version of traditional mural art. He visits the Holodeck where he has a "habak" program for the celebration of his people's ceremonial cycle.
As an adolescent, Chakotay pursued a vision quest, and in doing so obtained a "spirit guide" – a timber wolf – which appears to him now in dreams and visions, and often guides him in his decision-making process.
He has a reverence for all living things, and when he eats he offers thanks to the earth for providing food; he will not eat meat; he takes no drugs or alcohol.
As a leader he is steady, fearless, and capable of inspiring absolute devotion. Though he comes onto Voyager more by necessity than choice, he quickly wins the respect of even the most die-hard Starfleet veterans. He strikes an immediate and powerful bond with Janeway, and an unusual one with Kim, who through Chakotay's example begins to question his own homogenization and the loss of his traditional values.
=== Apocrypha ===
In the novel Pathways it is stated that the Starfleet captain who sponsored Chakotay in applying to Starfleet Academy was Hiromi Sulu, the grandson of Hikaru Sulu, while in the short story "Seduced" from the anthology Tales from the Captain's Table, it is stated that it was Demora Sulu. That Chakotay referred to this captain as a "he" is explained as a deliberate deception on Chakotay's part as he did not believe that his father would have the same respect for a woman as he would for a man.
Chakotay graduated from the Academy in 2351. By 2353, he served aboard the as an aide to Captain Roger Hackney and held the rank of lieutenant. It was aboard the Vico that Chakotay had his first encounter with a Cardassian warship that had violated the Federation border. In 2362, Chakotay transferred to the USS Gage where he stayed aboard for four years of conflict with the Cardassians. Following the end of the Federation-Cardassian War, Chakotay was granted an extended leave to his homeworld. By 2368, Chakotay was promoted to lieutenant commander and serving aboard the , under the command of Captain Madolyn Gordon.
Pathways also asserts that Chakotay's homeworld is called Trebus, but the relaunch novels assert that he and his family were native to Dorvan V which – as established in Star Trek Monthly Issues 4 and 10 (pages 55 and 14, respectively) – the producers of Voyager initially intended to be Chakotay's homeworld, even though that contradicts with Chakotay's year of birth of 2329 and the fact that Dorvan V became a colony in 2350.
Pathways references Chakotay originally having a room to himself at the Academy, before being roomed with a Bolian named Chert, and being put on report by a dorm officer for not having his bed made with a mitered corner. These details were also included in an article on Starfleet Academy in .
In the short story "Isabo's Shirt" from the Voyager anthology book Distant Shores, Chakotay would begin serving on the USS Heritage. where he and a female officer named Grant who was the first officer would begin a romantic relationship, one which Grant noted in Chakotay's Starfleet file. In 2375, the Voyager crew held a "roast" of Chakotay for his birthday and parts of his Starfleet record were read aloud, including Grant's note about their relationship.
In the Voyager relaunch book series, Chakotay returned to Starfleet. His activities as a Maquis were pardoned, and his provisional rank was made official. Through the efforts of the former Captain Janeway, now a vice admiral, he himself was promoted to captain and given command of Voyager where Tom Paris served as his first officer. Chakotay and Seven subsequently ended their romantic liaison. The series also showed his younger sister, Sekaya, who had become a spiritual leader of their tribe. 
In the Voyager novel Full Circle, Chakotay and Janeway finally admitted their feelings for each other and began a romantic relationship in 2379; they agreed to meet again in Venice after Voyagers return from the Yaris nebula the following year. When Chakotay traveled to Venice to meet Janeway, however, he was greeted by her former fiancé Mark Johnson who revealed the news of her death. Distraught, Chakotay made a questionable and out of character command decision on his next mission. This and other questionable command decisions resulted in Chakotay requiring a psychological evaluation and eventually resigning from Starfleet altogether. In the Voyager novel Unworthy Chakotay finally returned to Starfleet and was once again given command of Voyager. In The Eternal Tide, Chakotay resumes his relationship with Janeway when she is brought back to life by Q's son and Kes. 
In an alternate timeline illustrated in the Star Trek: Myriad Universes novel Places of Exile, Voyager was forced to remain in the Delta Quadrant due to serious damage to the ship and Chakotay became a statesman in the Vostigye Union, which had become Voyagers new home. In this timeline, he and Janeway were romantically involved and had a daughter named Shannon Sekaya Janeway.
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