Equinox , Part II ( episode ) Captain Janeway takes her quest for revenge against Captain Ransom to extremes when she orders the use of photon torpedoes against the " Equinox " , tractors a neutral ship , nearly kills an " Equinox " crewman during an interrogation , and relieves Chakotay of duty when he questions her actions . ( " Season premiere " ) Summary . Teaser . An attacking nucleogenic lifeform knocks Captain Janeway to the deck , but she manages to dodge the thermionic radiation . Yelling for tactical control , she uses a deflector pulse to reinforce the shields – at least , temporarily . The aliens ' attacks are halted , but damage has been done ; Chakotay is unconscious , and there ' s no response from sickbay . Ensign Kim reports two casualties due to the alien attacks . The , in the meanwhile , realizing that " Voyager " is under attack decides to maintain course and not charge to the rescue . With the multiphasic shield ing in place , the aliens are staying clear . Act One . Janeway , wandering the corridor s of the , comes across the remains of an alien killed in the attack , before being handed The Doctor ' s mobile emitter by Neelix , who found the device on Deck 9 . She takes it and reactivates the EMH back in sickbay , not realizing that it is the EMH program from the " Equinox " , whose ethical subroutine s have been deleted . " The Doctor " explains that when he was taken hostage by the " Equinox " he deactivated himself to escape . He begins by treating Chakotay , whom Tom Paris has managed to stabilize . While Janeway insists that they focus their efforts on finding the " Equinox " , Chakotay argues that they need to stop the attacks by the aliens first . While they are debating , they are interrupted by the sound of the interspacial fissures , which indicate the presence of the aliens . On the " Equinox " , Ransom tries to persuade Seven of Nine to stop resisting him and to become part of the crew , instead of spending her time in the brig for the remainder of the journey . Seven refuses to comply , however , telling him bluntly that he would be an inferior role model to her , and that " Voyager " made a mistake to trust him . While trying to treat Seven , Max Burke realizes that their EMH has left them a replacement , and activates The Doctor from " Voyager " . Seven and The Doctor realize they ' re stuck on the " Equinox " together . Meanwhile , the " Equinox " prepares to activate their enhanced warp drive , using the aliens as fuel to get back to Earth within several months . However , just as the ship is accelerating , it stalls . The power relay s to the modified injectors have been encoded – Ransom quickly realizes it must have been Seven of Nine . He tries to get her to give him the codes , but Seven refuses again . Burke suggests extracting the codes themselves if she won ' t give them . When The Doctor protests , Ransom simply deletes his ethical subroutines , and gets him to extract the information by any means necessary . On " Voyager " , Chakotay and Harry Kim have come up with a way that may allow them to communicate with the lifeforms . Despite misgivings , they drop the shields around the bridge and send the message . An alien appears , flies over to Kim ' s station and shrieks unintelligibly at the ensign for a moment , then disappears into its realm . However , the shields are attacked again . Another deflector pulse is activated , but it loses power quickly . Janeway , who is growing more impatient , gives an order to repair the warp drive so they can pursue the " Equinox " . When Chakotay asks to take another shot at the message to the aliens , she rudely dismisses him . Over in the ready room , Chakotay tells Janeway that he understands her anger towards Ransom who has betrayed everything the Federation and the uniform they are wearing stands for , but that she cannot compromise the safety of this ship to satisfy some personal vendetta . She tells him that she appreciates his candor , but that even so , she is not going to stand for Ransom continuing to murder and torture another lifeform so he can get home faster . She vows to hunt him down no matter how long it takes , no matter what the cost and if he wants to call that a vendetta , then he can go right ahead . Act Two . Ransom , who is hiding the " Equinox " in the atmosphere of a planet so they can make the repairs , checks in with The Doctor , who reveals that in order to access the information in Seven , he will have to remove her cortical array which contains an index of her memory engram s . By doing so , however , all of Seven ' s higher brain functions will be severely damaged . Ransom pleads with Seven to give him the codes , but she refuses . He says that doing this to her is not easy for him but that she leaves him no choice . Seven states that he uses that phrase quite frequently : destroying lifeforms to obtain his goals and then claim that they left him no choice . She stubbornly tells him that he will have to destroy her to obtain the codes . The Doctor proceeds . Chakotay is summoned to Janeway ' s ready room – she notes it ' s unlike him to submit recommendations in writing , holding up a PADD . Commenting on their last conversation he tells her that this was the only way he thought he could interact with her . However , Janeway refuses this suggestion , namely getting in touch with the Ankari , the race who introduced Ransom to the nucleogenic lifeforms , as well . She argues that this would take them off course and waste their time . She notes that from studying Ransom ' s service record , she found that he has the tendency to hide when he is being pursued . She asks Chakotay to use astrometrics to find likely hiding places , such as a nebula . " Equinox " , meanwhile , still in hiding in the planet ' s atmosphere which shields them from " Voyager " s sensors , continues repairs . Ransom sends Noah Lessing and Angelo Tassoni down to mine some dilithium while he takes a break to use his synaptic stimulator , a device which allows him to experience various alien vistas . The pair beams down , but is captured by a " Voyager " away team , Paris and Chakotay . On the bridge , the " Equinox " EMH tries to warn Ransom that " Voyager " has found them , and that they have polarized their hull to mask their approach . His communication gets cut off and Ransom orders for battle stations . Act Three . " Voyager " and the " Equinox " engage in a brief battle , " Voyager " taking the " Equinox " weapon systems off - line . Not willing to accept defeat , Ransom takes his vessel deeper into the planet ' s atmosphere . " Voyager " follows , but has to retreat when the deflector , which they are relying on to protect the vessel against the lifeforms , begins losing power in its attempts to protect the vessel against the atmosphere . " Equinox " escapes to warp , while " Voyager " is forced to repair its primary systems first before being able to pursue . Janeway interrogates Lessing , whom she has tied up on a chair in the cargo bay . She threatens to drop the shields in the room and let the aliens in if he doesn ' t tell her Ransom ' s tactical status . Getting nowhere with him , she goes outside with Chakotay , and drops the shields . Chakotay quickly realizes Janeway isn ' t bluffing , and asks her to stop what she is doing , that she is going too far ; she insists that Lessing will break while Chakotay states that he won ' t . When she refuses to do so , he first tries to raise the shield but finds only Janeway can . He then goes in himself and rescues Lessing , saving him in the nick of time . Telling Lessing that he has proved his loyalty to his captain to himself , compromises and has him tell everything he knows on the Ankari . Janeway clearly disapproves , but doesn ' t interfere . Janeway agrees to try and find a nearby Ankari vessel . When everyone else is dismissed from the briefing , however , she confronts Chakotay , telling him that even though in the past they had their disagreements , he still never openly opposed her . Chakotay argues that she almost killed Lessing today and that this wasn ' t about rules and regulations , but about right and wrong ; upon warning her that he won ' t let her cross that line again , she relieves him of duty until further notice . Act Four . " Voyager " pursues an Ankari ship , but it does not respond to Voyager ' s hails . Not having the patience to pursue normal diplomatic channels , Janeway orders Tuvok to use a tractor beam on the ship . Tuvok objects as the Ankari ship had done nothing , but she yells at him to " just do it " . The Ankari , who don ' t want anything to do with " Voyager " after what the " Equinox " did , are corrected in that " Voyager " did nothing wrong . The Ankari captain agrees to act as a translator for the " Spirits of Good Fortune , " but states that " Voyager " s crew will have to be the ones to convince the lifeforms . Speaking with them in the cargo bay , the lifeforms demand the destruction of the " Equinox " as retribution . It turns out they can perfectly understand the crew ; it is the crew that cannot understand them . Tuvok tries to persuade them that they will punish the " Equinox " crew in their own way , via imprisonment , but gets nowhere . The lifeforms don ' t believe they would harm their own kind . Janeway tells them the Federation has rules that the " Equinox " disregarded and unusually promises the lifeforms to deliver the " Equinox " to them if they stop their attacks on the " Voyager " . Now it is Tuvok ' s turn to object against Janeway ' s irrational behavior , reminding her the lifeforms will kill the " Equinox " s crew but Janeway makes him very much aware she ' s willing to confine him to quarters just like she did Chakotay . The lifeforms accept Janeway ' s offer . On the " Equinox " , Burke informs Ransom they need more " fuel , " using a euphemism to describe the dead aliens . Ransom points this out , with another moment of reflection on what he ' s doing . Burke notes the number they need , and Ransom then goes to the lab to see The Doctor . He ' s about an hour away from finishing with Seven , though he curiously finds The Doctor is singing with Seven , having triggered her responses . Ransom has another moment of reflection on having " no choice " when The Doctor points out Seven stood in his way of getting his crew home , giving him no choice . He leaves to escape the conflict he ' s in , to the synaptic stimulator . Although the stimulator is only designed to view landscapes , being nowhere as advanced as a holodeck , he sees someone in it : he is amazed to discover it is Seven of Nine , who asks , then demands that Ransom find another way home . Seven turns into a nucleogenic lifeform , at which point Ransom ends the program . Burke summons him to the bridge at the same time , as " Voyager " has found them again . Act Five . Ransom orders the starship to open a channel , preparing to surrender to Janeway and make peace with the aliens . Burke doesn ' t want to accept surrender , sends Ransom to the brig , and takes control of the ship . Marla Gilmore points her phaser at Ransom , and takes him away . Burke contacts the " Equinox " EMH aboard " Voyager " and asks him to find the vessel ' s current shield frequency . " Voyager " opens fire on the " Equinox " , and the two ships engage in combat while at warp . Gilmore leads Ransom to engineering , and lowers her phaser – confessing that she is on his side and wants this to end as much as he does . The two begin trying to access the transporter controls . " Voyager " destroys the " Equinox " port warp nacelle , and the ship falls out of warp , leaking plasma . " Voyager " continues to pursue , still firing its weapons . The EMH transmits the shield frequency to Burke . " Voyager " moves in , preparing to engage a tractor beam , while Burke manages to fire torpedo s through the shields . Despite Tuvok rotating the shield frequency every ten seconds , " Voyager " suffers extensive damage , losing many weapons arrays and the impulse drive . Ransom suddenly hail s the ship and tells Janeway he ' s ready to surrender , but Burke ' s mutiny left Ransom no longer in charge ; however he ' s isolated the transporter controls and that he can transport the " Equinox " crew to " Voyager " . He also advises her to have guards ready , as not everyone may be happy to see her . Amazed at their captain ' s sudden change in attitude , Janeway agrees . She tells her crew that Ransom is a Starfleet captain after all , even if he forgot that for a while . Burke isn ' t ready to surrender just yet , however , and places a force field around the bridge . On Ransom ' s order , Gilmore transports herself and two other crewmembers to " Voyager " , along with Seven of Nine while Ransom takes control of his ship ' s shield grid . They also transfer The Doctor ' s program back to his sickbay , with ethical subroutines restored . The " Equinox " EMH threatens to blow out every holoemitter in the room with planted photonic charges set to a command sequence ; however the " Voyager " Doctor simply deletes him , thus stopping his transmissions to the " Equinox " . Ransom , still in engineering , contacts his bridge . He tells the stunned Burke that he has dropped the shields around the ship , except the bridge and his current location . The vital systems are exposed . Burke refuses to transport to " Voyager " , despite his captain ' s pleas – instead , he tries to lead the bridge crew to the nearby shuttlebay two decks down , but all perish en route . As the lifeforms attack the " Equinox " warp core , Ransom hails Janeway . He tells her that his ship is about to explode , and he has to get it to a safe distance from the immobilized " Voyager " . Janeway tries to get Ransom off , asking him to set auto - navigation . He refuses , saying he has no time . He tells her that she has a fine crew and has her promise him to get them home . Having set a course away from " Voyager " , he wears his synaptic stimulator one last time , looking at a beautiful beach . A moment or two later , " Equinox " explodes , and the Captain goes down with his ship . In the briefing room , after dressing down and harshly rebuking the five former and surviving " Equinox " crew members ( Noah Lessing , Marla Gilmore , James Morrow , Brian Sofin and Angelo Tassoni ) , Janeway strips them of rank , telling them that from now on they will serve as crewmen on " Voyager " , their privileges will be limited , and they will work under close supervision for as long as she deems fit . They will need to earn her trust this time . They are escorted away by Tuvok . Heading out the other way onto the bridge with Chakotay , the subdued Janeway wonders how the crew is doing . Chakotay says that Neelix has organized a potluck to boost morale . In a silent moment , she tells him that he may have had good reason to stage a little mutiny of his own . Chakotay admits that the thought had occurred to him , but that it would have been " crossing the line . " This strikes a chord with the captain who reflects upon how close her recent actions had come to being no better than that of the " Equinox " and Captain Ransom . She then notices the dedication plaque of " Voyager " that has fallen down for the first time in all these years . Wiping it off , Chakotay suggests putting it back where it belongs – mirroring the earlier fall of the " Equinox " plaque and a similar conversation she had with Ransom . . . Memorable quotes . " " You destroy lifeforms to attain your goals then claim that they left you no choice . Does that logic comfort you ? " " " Please state the nature of the . . . " [ looks around ] " don ' t bother . " " " " You know , Janeway ' s not the only one who can help you explore your Humanity . " " " " You would be an " inferior " role model . " " " " This man betrayed Starfleet . He broke the Prime Directive , dishonored everything you believed in , and threw " Voyager " to the wolves . " " " " Kazon , Vidiians , Borg , Hirogen , Malon . We ' ve run into our share of bad guys . Ransom ' s no different . " " " " Yes , he is . You said it yourself . He ' s Human . " " " " We ' ve almost got him . One more torpedo ought to do it ! " " " " Captain – " " " " Fire ! " " " " What the hell is he doing ? Follow him ! " " " " We all make our own Hell , Mr . Lessing . I hope you enjoy yours . " " " " Do these programs have people in them ? " " < br > " " No , just landscapes . " " " " I ' m warning you : l won ' t let you cross that line again . " " " " Well then you leave me no choice . You are hereby relieved of duty until further notice . " " " " What ' s happened to you , Kathryn ? " " " " I was about to ask you the same question . " " " " Tractor beam . " " < br > " " Captain , the Ankari ship has done nothing to . . . " " < br > " " Just do it . " " " " I will summon them , but " you " must talk to them . " You " must convince them . " " " " They say , they want the Humans to die . " " < br > " " A difficult place to start a negotiation . " " " " This isn ' t the brig . " " " " I know . I ' m with you , sir . Let ' s find a way to end this . " " " " He ' s still a Starfleet captain . He may have forgotten that for a while but I believe him . " " " " What are you doing here ? ! " " " " Taking back my sick bay ! " " " " Your doctor is no longer on call . " " " " You ' ve got a fine crew , captain . Promise me you ' ll get ' em home . " " " " I promise . " " " " It ' s quite disconcerting to know that all someone has to do is flick a switch to turn me into Mr . Hyde . " " Links and references . References . amputation ; Ankari ; Ankari vessel ; auditory processor ; brig ; class 2 nebula ; confined to quarters ; cortical array ; cortical node ; crouton ; decihertz ; dedication plaque ; deflector pulse ; " Dem Bones " ; demotion ; deuterium ; Earth ; Epsilon IV ; ethical subroutine ; gas giant ; ground squirrel ; holodeck ; Hyde ; inertial damper ; interspatial fissure ; kilometer ; Klingon s ; Klingon Bird - of - Prey ; logic ; McKinley Park ; memory engram ; meter ; morality ; " My Darling Clementine " ; nebula ; neural interface ; ; nucleogenic lifeform ; nucleogenic particle ; occipital node ; ocular node ; olive branch ; parthogenic atmosphere ; photon torpedo ; photonic charge ; poison ivy ; polarized hull plating ; potluck ; power core ; power relay ; reticular node ; Regellian blood worm ; role model ; Romulan warbird ; salad ; sensory node ; ; shield frequency ; synaptic stimulator ; Tenkaran coast ; Terrelian seapod ; torture ; tractor beam ; Ransom ' s personnel database references . Klingon Bird - of - Prey ; Romulan Neutral Zone ; T - Tauri type ; Zaphod sector