Chakotay Chakotay was a 24th century Human Starfleet officer and former Maquis member , best known as first officer under Captain Kathryn Janeway aboard the . Before serving as " Voyager " s first officer , he had resigned from Starfleet after years of service in order to join the Maquis to defend his home colony against the Cardassian s . In 2371 , while Starfleet and the Cardassians were trying to capture him in the Badlands , Chakotay and his Maquis crew were pulled 70 , 000 light year s across the galaxy , deep into the Delta Quadrant by the Caretaker ' s array and forced to merge with the crew of the " Voyager " during its seven - year journey home . ( ) Early life and family . Chakotay was born in 2329 on a Federation colony near the Cardassian Demilitarized Zone that his native tribe had moved to several generations earlier . Here , he was raised by 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 hear any of that 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 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 , at that time , 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 quest s 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 hallucination s 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 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 asteroid s 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 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 ( ) and went on to serve aboard a Starfleet ship . He recalled once visiting a tomb excavation on Ktaria VII on one of his earliest away mission s . 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 . ( ) Another of his earliest missions was being on a diplomatic team to make first contact with the Tarkannan s . After spending a lot of time pushing his captain to let him be on the 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 Drayan s . ( ) 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 . On March 3 , 2368 he resigned from his position as an instructor in Starfleet ' s Advanced Tactical Training by submitting his resignation to Admiral Namimby . Some time later he joined the Maquis . ( ) After joining the Maquis , he became one of its leaders and his became one of the most successful in resisting the Cardassians and Federation . Chakotay was one of the Maquis who were in the fight for principle , not mercenary gain or violent outlet . ( ) USS " Voyager " . While trying to escape from a Cardassian warship piloted by Gul Evek in the Badlands , Chakotay and his crew , including B ' Elanna Torres and 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 . ( ) 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 Caretaker . 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 , the " Val Jean " , into a Kazon carrier vessel . Following the destruction of his ship in the Delta Quadrant , Chakotay and his crew joined " Voyager " s crew as one Starfleet crew in order to find a way home . He was granted the provisional rank of Commander and became " Voyager " s second in command . A man of great moral conviction and courage , Chakotay embraced Starfleet principles once again and served Captain Janeway as first officer – eventually being able to forge a meaningful friendship with her ; his loyalty never wavered and he helped keep the peace and establish cooperation and a positive rapport between his Maquis and the Starfleet crew . ( ) The first year ( 2371 ) . During their first year in the Delta Quadrant , his shuttlecraft was attacked by the Komar 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 code s . With his presence confirmed , he subsequently used a medicine wheel that Torres had placed in sickbay to provide the crew with a map out of the nebula . The Doctor later developed a treatment that returned his mind to his body . ( ) His devotion to " Voyager " and Starfleet were strong ; he even threatened to throw Seska and Jarvin into the brig when they said they would support him in a mutiny . 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 " . ( ) 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 ( ) 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 had 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 as he not only 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 . Seska shortly after escaped from the ship and joined Maje Culluh of the Kazon Nistrim . ( ) The second year ( 2372 ) . 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 Spirit s . 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 . ( ) The same year , Chakotay and Janeway were infected with an incurable virus which necessitated them being left behind on a planet whose environment somehow could halt 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 third year ( 2373 ) . After " Voyager " traveled back in time to 20th century Los Angeles on Earth to stop Henry Starling from stealing a time ship , 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 archeology 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 , although they were then simply returned to the future in the Delta Quadrant by an alternate Braxton who never experienced these events . ( ) 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 just like 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 . They asked Chakotay to help them by activating the neuroelectric 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 help 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 – 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 fact of that kind of power . ( ) The same year , Chakotay became involved in the Distant Origin Theory controversy among the Voth , a saurian species that believed to be native to the Delta Quadrant . Forra Gegen , a leading Voth scientist , 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 dinosaur s on Earth . When the evidence was presented to the Voth council , Chakotay stood with him to support his evidence . The council rejected it 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 . ( ) 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 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 . ( ) The fourth and fifth years ( 2374 - 2375 ) . 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 scenarios of innocent Vori being killed and tortured . He became so embittered that he turned into a killing machine , but he was rescued by Tuvok and convinced of the brainwashing before he could complete his first true mission . ( ) 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 , he 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 hold on to his faith . ( ) Chakotay saved " Voyager " from the Dream species : 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 interaction with the aliens . He eventually found that a large transmitter was responsible for the dream state the entire crew found itself to be . He told The Doctor to deploy a torpedo at the cavern , and the alien leader was forced to neutralize the transmitter , which woke the crew and freed them from alien control . ( ) Chakotay also encountered Species 8472 again , when " Voyager " discovered an Earth - like structure on a planet . 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 . He became romantically involved with one of the aliens who had assumed the identity of a Starfleet lieutenant commander named Valerie Archer . ( ) He also encountered aliens when " Voyager " became trapped in chaotic space . Chakotay saw the faces of his friends as the aliens who told him how to guide the ship out of chaotic space before it was destroyed by the anomaly . ( ) 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 lifeform s as fuel for their special warp drive ; an act that appalled Janeway unimaginably , 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 in numerous occasions , 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 by Starfleet rules . When she finally came to her senses she realized how she had crossed the line herself and that Chakotay certainly had good reason to stage a mutiny of his own . ( ) The sixth year ( 2376 ) . " Voyager " helped defeat the Vaadwaur , a confrontational and treacherous species that was revived after over eight - hundred years in stasis . They were revived with good intentions but when they began turning on Janeway and her crew , she realized that she had made a fatal move . Chakotay had warned Captain Janeway earlier and was leery of awakening the Vaadwaur , 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 , however , Chakotay was injured and had to remain on the " Delta Flyer " while the task of retrieving the command module fell on Seven of Nine , who did not share Chakotay ' s or anyone else ' s enthusiasm for such sentimental attachments to history . Chakotay did express his envy when he realized that he could not beam on board the " Ares " but insisted that Seven download everything she could while she was there " touching history " . ( ) During one of The Doctor ' s " daydream " programs , an alien species who had been spying on " Voyager " accidentally tapped into The Doctor ' s program and believed his fantasies to be the reality . In The Doctor ' s imaginations , Chakotay was attacked by the Borg and about to be turned into a drone . ( ) In the same year , when Seven overloaded her Human brain trying to download too much information at once and became delusional about possible conspiracies aboard the ship , Chakotay and Janeway almost came into conflict when she told them two competing conspiracy theories . ( ) Chakotay suffered from violent dreams that put him in the middle of a massacre that killed innocent civilians and about the cover - up that followed after an away mission . This was a result of a synaptic transmitter in a structure on the planet that sent neurogenic pulses that caused memories of the massacre to be implanted on anyone who came near the structure . It was a memorial to the victims and a reminder to never let such a massacre happen again . ( ) The final year ( 2377 - 78 ) . In 2377 , the last year before " Voyager " s return to the Alpha Quadrant , Chakotay attempted to hijack " Voyager " with his former Maquis crew due to a mind control suggestion implanted into Tuvok by a Bajoran Vedek named Teero Anaydis . ( ) Later that year , he also restored " Voyager " to the proper timeline when it was hit by a chronokinetic surge from a spatial rift . ( ) He also rescued the crew from the workforce when the crew ' s memories were wiped out in order to solve the workforce shortage on Quarra . For that , he assumed the identity of Amal Kotay . In the Central Power Facility , Chakotay displayed expertise in thermionic conversion , but it was revealed he had only moderate knowledge of microkinetics . After Chakotay and Neelix took Torres back to " Voyager " . ( ) Chakotay was able to lose the Quarren guards . He then tried to convince Captain Janeway to help , but she turned him over to the authorities . Chakotay was then taken to Dr . Ravoc , where Chakotay was brainwashed and ordered " Voyager " to rescue him and the rest of the crew . Chakotay and the rest of the crew was then rescued and resumed their voyage home . ( ) Near the end of " Voyager " s time in the Delta Quadrant , he became romantically involved with Seven of Nine . They became very close during an away mission when they were stranded on a planet due to a shuttle crash . They discovered a primitive tribe known as the Ventu , that helped them contact their ship . ( ) The return home . Chakotay returned to the Alpha Quadrant with the rest of the crew using a Borg transwarp hub . Admiral Janeway returned to the past to help her counterpart , Captain Janeway , defeat the Borg and return the ship sooner than the twenty - three years it originally took her . This saved the life of Seven , who had been killed on the original journey home , and helped Tuvok avoid a mental breakdown due to a neural disease . ( ) 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 shuttle craft 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 " Voyager " s 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 drone s , 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 . ( ) Alternate Timelines . During the " Year of Hell " conflict with the Krenim , 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 " Voyager " { ' } } s 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 off line . 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 " Delta Flyer " to map the slipstream in advance of " Voyager " to monitor potential instabilities in the slipstream matrix as it formed . As a result , 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 before setting out to find " Voyager " , salvaging The Doctor ' s program and Seven ' s corpse with the goal of sending modified slipsteam calculations back to before " Voyager " was destroyed so that the ship could make it home . Despite the interference of Captain Geordi La Forge and his ship , coupled with damage to 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 . ( ) Personal interests . Chakotay didn ' t use the holodeck often , but enjoyed reading instead . ( ) 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 . ( ) Foods . Chakotay was a vegetarian ; one of his favorite meals was mushroom soup . Some foods he hated were carrot s and fried food ( because it upset his stomach ) , and he refused to eat pudding because he thought it was slimy . ( ) Chakotay preferred to avoid alcoholic beverages when possible , saying he preferred to " stay in control " , but was known to imbibe on special occasions . For example , he kept a secret stash of Antarian cider hidden among the salvaged Borg components in cargo bay 2 . ( ) 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 " Voyager " s visit there in 2373 ( 1996 ) , and said that if they were trapped there , maybe he ' d 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 . ( ) In 2375 , while the telepathic pitcher plant made most of the crew believe they were going to reach Earth through a wormhole , Chakotay imagined he ' d received a full pardon – 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 and damaged the " Flyer " 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 , 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 in the search . ( ) Later that year , he was very interested in a planet they discovered that moved at an accelerated rate compared to normal space - time . He had " Voyager " send down a probe to take images as the planet advanced . 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 . 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 , " Voyager " came across a game called " Tsunkatse " on Norcadia Prime . He was quite a fan , and was sure to watch several of the matches live . Although The Doctor didn ' t approve , 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 day one 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 , she could not imagine a day without him . The mutual respect they had for each other was never lost even when they occasionally disagreed quite vehemently over command decisions . ( ) 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 . 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 as his captain and they shared an intimate moment after their conversation , holding hands across the table . After a cure for their illness was found and they were finally rescued , they agreed that certain things were better left behind on the planet , and resumed their respectful and cordial relationship . ( ) 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 " Voyager " s 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 . 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 star s 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 . ( ) 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 lifeform s 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 stroke 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 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 male characters of the " Fair Haven " program created by Tom Paris . ( ) When a Janeway from another timeline asked him about their relationship in the future , he simply replied that there were some barriers they never crossed . ( ) . 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 . ( ) " Voyager " s 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 off line . 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 initially came up to her jokingly " " Is there something different ? You seem to be glowing today . " " She immediately knew someone had told him . Chakotay was hoping to be the child ' s godfather , and even suggested several names – such as Taya , the feminine form of Chakotay . ( ) 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 . The two eventually made it out safely , and Chakotay joked to the captain when they returned that he ' d be " Paris ' personal body guard , " as he owed him ever since he saved his life . ( ) 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 he called on his unacceptable behavior . He also loudly expressed his negative opinion on Chakotay ' s role as first officer in " Voyager " s 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 . ( ) 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 which landed him 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 thruster s . 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 lead to the capture of the " 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 lead 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 xenophobic species , 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 hand writing down his memories of her visit , so they wouldn ' t be forgotten . ( ) 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 implant s 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 flower s 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 " Voyager " s 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 , they set a course back to the Demon class planet , but everyone , including the duplicate Chakotay , died before the ship could reach home . ( ) Holographic recreations . Chakotay was holographically duplicated on a number of occasions : 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 " Voyager " s return . According to Admiral Janeway , shortly after " Voyager " s 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 . ( ) Memorable quotes . " " I ' m going to try and take some heat off your tail . " " " " I have no intention of being your token Maquis officer ! " " " " We talk to animals . " " " " You were working for her , Seska was working for them , was anyone on that ship working for me ? " " " " My people taught me a man does not own land . " " " " Flattery , devotion , sex . . . I thought she had a lot to offer a man . " " " " 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 ! " " " " Breathe , damn it ! Breathe ! " " " " She . . . bit you ? " " " " I ' m not letting anyone implant some neural processor in my brain ! " " " " What ' s the matter ? Our galaxy wasn ' t big enough for you ? " " " " Motherless beast ! " " " " Never spar with a Vulcan . " " " " Maybe you can just flip some Borg switch and shut down your emotions but " I " can ' t ! " " " " This is perfection . " " Appendices . Background information . The Native American character that became Chakotay was one of the first characters devised for . 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 . " " ( " " , 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 . " " ( " " , 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 " . ( " " , pp . 188 - 189 ) To find out more about the character ' s Native American background , the producers enlisted the assistance of Jamake Highwater . ( " " , 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 . ( " " , 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 " . ( " " , p . 208 ) Chakotay was the first person to be seen on " Star Trek : Voyager " s series premiere , . In the first draft script of that episode , he was described as " an intense Native American man in his late thirties " and with " a tattooed face . " At the end of the script , he was promoted to the rank of lieutenant commander instead of becoming a full commander . 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 . Although Chakotay was invariably referred to as " commander " during the run of the series , he wore what otherwise figures to be the provisional rank insignia of a lieutenant commander ( two solid stripes , one hollow stripe ) . He is , however , listed as " Commander Chakotay " in the opening credits of virtually every episode from the first three seasons ( bar " Caretaker " , where no character ' s rank is given except Janeway ' s ) . In " " episode , the lieutenant commander who Ro Laren refers to as her instructor at Advanced Tactical Training in 2369 / 2370 , and who joined the Maquis , was intended by the producers as a reference to Chakotay . In fact , this information is included in Ro Laren ' s biography at StarTrek . com . That intention was contradicted in the " Voyager " episode , in which Chakotay stated that he resigned his commission on March 3 , 2368 . According to StarTrek . com ' s biography on Chakotay , he resigned his commission in 2370 . However , the same biography also lists his father dying in 2370 ( which sparks Chakotay ' s resignation ) and , later in the same article , that his father dies in 2371 ; it would seem that there is some confusion as to this . No surname is ever given to Chakotay , and it is unclear whether Chakotay is his given name or his family name . This makes him the only Human main character in the history of " Star Trek " with only one name . 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 , 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 " 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 " Voyager " s 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 " 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 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 . " 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 . In an alternate timeline illustrated in the " " 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 " Voyager " s new home . In this timeline , he and Janeway were romantically involved and had a daughter named Shannon Sekaya Janeway .