The opening scene takes place in a cryogenic lab on the mother ship. The labs have been experiencing inexplicable power surges and the technician on duty has instructions to monitor individual cryogenic chambers for surges and to watch diligently for any changes.

At Resistance Headquarters, Augur demonstrates to Liam that his computer system is now linked to the air traffic control system on the mother ship. Liam is curious to know if Augur broke into the system himself, and for a moment Augur ignores Liam's question, saying that he can now monitor all incoming and outgoing traffic. Liam persists, saying that Sandoval has just reprogrammed all the security codes and asking again if Augur has broken them already. Augur finally admits that he got the new codes from Lili, but says that he is the one who knew how to use them once they were acquired. After a few jocular comments Liam leaves to pick up Da'an on the mother ship. After he leaves Augur makes a comment to the empty room about Liam being jealous.

In the cryogenic lab, the duty technician hears a noise in one of the chambers and goes to take a closer look through the window in the chamber's door. The instruments in the lab suddenly go berserk with flashing lights and alarms, but the technician continues to stand peering into the cryogenic chamber. There is some movement inside the chamber and as the technician steps away, the glass window shatters and a figure emerges.

The escaped occupant of the cryogenic compartment is a Jaridian, and he manages to make his way to the shuttle bay where he sees Lili sitting at the controls of a shuttle and performing maintenance checks.

On the bridge of the mother ship, Da'an tells Zo'or that he must provide the Synod with the details of all active Taelon research programs. Zo'or remarks that Da'an is the only member of the Synod to have made such a request and says he will have Sandoval deliver a detailed report to Da'an. Da'an asks Liam, who has been waiting quietly nearby, to ready his shuttle and says that he will wait for Sandoval's report. Liam leaves for the shuttle bay, and Sandoval leaves to prepare his report for Da'an.

In the shuttle bay the Jaridian is watching Lili who is unaware of his presence. She tells the technicians that the shuttle's ID drive is scheduled for maintenance, then rises and moves to the rear of the shuttle. The Jaridian is waiting at the back of the shuttle and seizes Lil, disarming her and dragging her back to the cockpit where he orders her to fly him out of the mother ship. As the frightened Lili powers up the shuttle, the Jaridian places his hand around her throat to restrain her from taking any defensive action.

On the bridge Zo'or and Sandoval get word that the Jaridian has escaped from stasis and gone to the shuttle bay area. Sandoval orders all available security forces to go there at once.

Liam overhears Sandoval's transmission and moves to the shuttle bay where he discovers that the shuttle containing Lili and the Jaridian is already on its way out of the mother ship. He contacts Sandoval to tell him that the Jaridian has stolen a shuttle and taken Lili hostage. Then he jumps into a nearby shuttle and pursues Lili and the Jaridian. Sandoval asks Liam to supply them with a video feed so that his progress can be monitored on the bridge.

Lili asks the Jaridian for a destination or coordinates, but he roars, "Silence!". He removes his hand from around her throat and programs the coordinates of their destination into the shuttle console himself. Liam is in the second shuttle behind them in hot pursuit, and Lili tells this to the Jaridian who orders her to take evasive action.

On the bridge of the mother ship Zo'or orders that the Jaridian must be killed. Sandoval orders Liam to destroy the shuttle as soon as he can lock onto it. Liam starts to tell Sandoval that Lili is on board and that he is going to try something, when he is interrupted by Sandoval telling him to fire and that Lili must be sacrificed. Liam tries to lock onto the shuttle, but Lili is an expert pilot and is adept in the art of evasive shuttle manoeuvres. The Jaridian tells her to activate the ID drive and shows her where they are headed. At that same moment Liam locks onto Lili's shuttle and follows them into ID space, firing a blast which (intentionally) misses the shuttle as he goes.

Zo'or is furious that Liam's shot failed to hit the shuttle. Sandoval makes excuses for Liam saying that Lili's shuttle jumped into interdimensional just as Liam fired. He tells Zo'or that both shuttles are now out of communication range.

In ID space, the two shuttles are encountering some turbulence and being pulled off course by some kind of gravitational or tractor beam. When Lili's shuttle comes out of ID space, Liam is still in pursuit. The Jaridian asks Lili if she can get a shot at Liam and she tells him that she can't even steer as the two vessels are pulled inexorably toward a huge alien craft in the distance.

Lili's shuttle is the first to land within the strange ship. She notes (and informs the Jaridian) that the shuttle's controls do not respond and that its power appears to have been drained. The Jaridian leaves the shuttle and orders Lili to follow him. She asks him what his plan is and he tells her that they will destroy the device which is causing the power drain and continue on to their destination. The Jaridian is not familiar with the alien craft and asks Lili if she recognizes it. Lili looks around her before telling him that she has never seen anything like it. As he grabs her forcefully and pushes her down the corridor, she asks him how he learned to speak her language. The Jaridian tells her he learned from his years of captivity and from listening to humanity talk as they carried out their experiments on him. Lili, knowing that the Jaridians are actively trying to acquire ID space travel technology, asks him if it is the ID drive unit he is after. He tells her that when he reaches the Jaridian home world with the new ID technology, the Jaridians will return to earth in force and the Taelons will be wiped out. He pushes her forward again.

When his shuttle lands inside the alien craft, Liam leaves it and looks around, sensing something familiar about the place. There are symbols carved on the walls of the corridor, and he places his hand over one for a moment and closes his eyes. When he opens his eyes, it is obvious that he understands the nature of the alien craft. Then he follows Lili and the Jaridian.

The Jaridian and Lili approach a corridor which is flooded waist deep. They begin to wade through it and are close to the middle when they are attacked from beneath the surface by what seems to be a serpent or eel. The Jaridian pushes Lili to safety against the wall and fires his Sha'karava at the creature, then he seizes Lili and pushes her forward again. At the end of the corridor they step out of the water safely.

Behind them Liam enters the flooded corridor.

The Jaridian believes that the alien ship was created by the Taelons, but Lili does not agree because it bears no resemblance to the Taelon designs she knows so well. The Jaridian asks Lili why he should trust someone who works for the Taelons and grabs her roughly, growling that he should kill her. Lili has had enough of his rough treatment and tells him rebelliously to do it and kill her now. The Jaridian is surprised that Lili does not fear death. She tells him that she is a soldier, has been to war and does not fear death. The Jaridian makes the assumption that Lili was fighting the Taelons, and when he is told that she was fighting other human beings, he is disgusted, asking her what kind of animal kills its own kind. He circles Lili, looking at her from all angles and remarks that he finds it a contradiction that a being of such a strong aggressive nature could exist in such a fragile shell. Lili inquires whether Jaridian women go to war, and the Jaridian tells her that on his planet male and female fight side by side as equals and as they should. Lili asks him if he is a soldier, and he tells her that like all Jaridians he is a soldier, because that is what the Taelons have forced them to be.

Liam is wading through the flooded chamber and hears the serpent moving but he is unable to see anything in the darkness. Suddenly the serpent attacks him and he grapples with it.

The Jaridian hears the noises coming from the flooded chamber behind them where Liam is struggling with the serpent and decides the Taelons are following them. He and Lili conceal themselves against the wall of the corridor and wait for the enemy to arrive.

On the mother ship Da'an tells Zo'or that the Jaridian should never have been brought to the mother ship. Zo'or defends himself by saying that the information will be invaluable when the Jaridians arrive on earth. Da'an tells him that holding the Jaridian for so long was bound to be disastrous and his warning should have been heeded. Zo'or is confidant that the Jaridian will be captured. Da' an asks what the consequences will be if the Jaridian escapes with the interdimensional technology and rebukes Zo'or for behaviour unworthy of a leader of the Synod. Then he leaves.

Liam climbs out of the flooded chamber and sees more symbols carved on the walls. As he looks, the Jaridian fires his Sha'karava, but Lili calls a warning and Liam is able to evade the blast. The Jaridian shoves Lili hard and she tumbles to the floor beside a skeleton, banging her head as she falls. Liam and the Jaridian tackle each other violently and Liam is getting the worst of it when suddenly his own Sha'karava begins to glow. The astounded Jaridian picks Liam up and questions him. Liam tells the Jaridian that the Sha'karava is a gift from his father and that he himself is part Kimera. The Jaridian accuses Liam of lying because there are no Kimera left and there have been no Kimera for millions of years. Liam asks him how else he can explain the presence of Liam's Sha'karava. When the Jaridian accuses Liam of boarding the ship to kill him, Liam tells him that he could have killed him from his shuttle easily before the jump was made to ID space. He also tells the Jaridian that the ship is a Kimera ship and that he (the Jaridian) will need Liam's help if he wants to leave it alive.

The Jaridian releases Liam and Lili lurches to her feet and joins them. Liam tells them that the ship felt familiar to him when he first saw it. Lili thinks that the ship is a war cruiser, but the Jaridian says definitively that the Kimera would never have built a war ship. Lili asks Liam if he can read the symbols carved on the wall. He can read them easily and tells them that this is a repository ship which holds the accumulated knowledge of the entire Kimera race. This does not make sense to Lili because the ship literally kidnapped them by dragging them aboard, then tried to kill them. There re no easy answers to these questions and the Jaridian is anxious to get off the ship. Liam says that it should be possible to leave whenever they wish to because the ship was designed purely to test those seeking the knowledge of the Kimera and not accidental visitors. Lili remarks that the ship is holding them against their will, and Liam suggests that the ship's programming may be damaged.

They decide that the ship has devised a series of physical and psychological tests to determine whether a knowledge seeker is worthy to be allowed into the core of the repository. Lili points to the skeleton and tells Liam that what they have been put through is not merely a test, but a matter of life and death. Liam says that the only answer is that the ship's programming has been damaged. The Kimera race were not killers. Liam, Lili and the Jaridian decide to make it to the ship's core and figure out their strategy from there.

Zo'or tells Sandoval that he wants him to hunt down the Jaridian by shuttle. Sandoval tells Zo'or that he can be more effective by coordinating the search from the bridge. Zo'or points out that Sandoval is responsible for security on the mother ship and is therefore ultimately responsible for the Jaridian's escape. He tells Sandoval that the Synod will not be merciful to either of them, and he asks cunningly if Sandoval trusts Lili and Liam to kill the Jaridian.

As they move toward the core of the ship, the Jaridian asks Liam if the ship created the serpent which attacked them in the flooded chamber. Liam tells him that the obstacles are created to test their reactions to danger. Lili aks the Jaridian how he was captured and he tells her that he was on a deep space patrol when his ship was caught in a planetary gravitational field which caused him to crash on an asteroid. He was near death when the Taelons found him and captured him, locking him in a stasis chamber for their experimentation, and depriving him of the honourable death which he felt he deserved.

On the mother ship Da'an interrogates Zo'or, asking him if he denies allowing human technicians access to the Jaridian. Zo'or thinks such access was necessary. Da'an tells him that his actions were in direct violation of the Synod edict that no human being shall be exposed to the Jaridians. Zo'or replies that as leader of the Synod, he has broad discretion in how he manages Taelon affairs. Da'an accuses Zo'or of unprecedented arrogance and demands that the Synod consider his removal as leader. Zo'or replies that his priority is to kill the Jaridian and when that has been done, Da'an will have no basis for his demand. Da'an is insistent that the damage has already been done. Zo'or cannot understand and Da'an asks him pointedly what humanity will actually see when they look into the eyes of a Jaridian for the first time. Will they see the creature portrayed by the Taelons as evil incarnate, or will they see someone much like themselves?

The Jaridian is not sure they are going the right way to get to the core of the ship, but Liam reassures him that they are. They enter yet another corridor and the Jaridian stops suddenly sensing a trap. Lili sees a skeleton lying in the corridor and asks how he was killed.

In reply, the Jaridian pulls one of the Kimera symbols off the wall and hurls it down the corridor. The symbol has not travelled very far when it is hit by a laser beam and disintegrates. Liam offers to go first, but the Jaridian steps forward. His eyes begin to glow as he activates some kind of infra red vision which allows him to see the invisible laser beams crisscrossing the corridor. He makes his way forward the end of the corridor, timing his moves very carefully. Lili asks Liam about the Jaridian's ability to enhance his vision. The Jaridian almost gets to the end of the corridor and safety, but as he approaches the end, he makes a hasty move and one of his wrists is caught in a laser beam.

The corridor is a dead end and the Jaridian is starting back toward them when the wall behind Liam and Lili begins to move forward sealing the exit shut behind them. Liam is able to remember the steps the Jaridian took and he and Lili move down the corridor in unison. When they reach the end, every wall starts to move, threatening to crush them. There is nowhere to go but up, and all three scramble over the top of one of the walls, Liam boosting Lili, the Jaridian boosting Liam, finally the Jaridian who is pulled up by Liam and Lili together using Liam's belt.

Lili examines the Jaridian's wrist wound and binds it taking a scrap of cloth from a nearby skeleton. The Jaridian would prefer to do it himself, but reluctantly lets Lili bandage his wrist.

Sandoval has reluctantly boarded a shuttle and is searching through space for the Jaridian.

On the Kimera ship, Lili asks the Jaridian why his race are hunting the Taelons. The Jaridian tells her that the Jaridians and Taelons are genetic brethren who were once one race and split up over the Sha'karava. The Taelons were unable to control the dark side of the Sha'karava and renounced it in their quest for spiritual perfection. Liam asks if the Jaridians are not also afraid of the Sha'karava and is told that the Jaridians were more afraid of the Commonality. The Jaridian tells them that his race did not wish to lose their passion, their joy, their ability to love, to hate, and to reproduce. Lili is surprised to learn that the Taelons cannot reproduce and the Jaridian tells her that in their quest for spiritual perfection, the Taelons failed to realize that they were on the path to eventual extinction. The Taelons are dying out but the Jaridians continue to flourish and multiply. The Taelons are desperate to recombine the two races and regain what they lost, but at the expense of the Jaridians. Liam asks why the Jaridians are hunting the Taelons and the Jaridian replies, . "Because they are hunting us. They wish to use humanity as the tool to bring us to our knees."

Sandoval reports back to the mother ship that he has not located the Jaridian and Zo'or tells him that he has only one hour to do it because Da'an has convened a meeting of the Synod to petition his removal as leader.

Liam, Lili and the Jaridian enter a chamber in which there is a large hole or trapdoor in the floor with a rope descending into it, but they can see nothing in the darkness below. Lili wants to find another way to exit the chamber, but Liam volunteers to go below. The rope does not reach the floor of the chamber below and Liam lets go of its end, falling the rest of the way to the floor. There he finds the doorway for which they have been searching and recognizes it by its description because of the Kimera writing on the walls of the ship.

Liam goes to the door and moves the Kimera symbol inscribed on its face. Suddenly there is an explosion and Liam is thrown to the floor unconscious. The others who are still above Liam call down to him and when there is no answer, they descend quickly. Liam is not breathing and Lili tries to revive him with CPR. The Jaridian is puzzled and watches her, asking why she tries so hard when he thought she did not fear death. The impassioned and frantic Lili replies that Liam is her friend and that he is humanity's best shot against the Taelons and the Jaridians - if it comes to that. The Jaridian reaches out to help her with Liam and Lili fiercely tells him to stay away, but he pushes her aside and uses his Sha'karava to administer a mild shock which revives Liam. Liam sputters and sits up, asking what happened. Lili tells him that an explosion almost killed him, but the Jaridian revived him and saved his life. Liam offers his hand to the Jaridian and tells him that he owes him one. The Jaridian is embarrassed and perplexed by the gesture. He tells Liam that he is owed nothing and that they need each other to get off this ship.

A light is shining from within the open door and they pass through it into a chamber which contains a large sphere. Liam places his hand over one of the symbols and it begins to glow. He tells his companions that it is a welcome and says that the ship will make itself known when...... His voice trails off as the sphere begins to glow and a strange female entity emerges from it. The entity explains that she has taken a human form in order to communicate with them. She has watched their journey through the ship and they demonstrated sacrifice, bravery, and strength during their passage, but the final judgment of the ship is that they are not ready to receive the Kimera wisdom. The Jaridian insists loudly on having the information. Liam says that they accept the judgment which has been rendered and merely want to get off the ship. The entity tells him that she has not yet completed her study of their species. The Jaridian demands that the wisdom of the Kimera be shared with him immediately so that he can take it back to his fellow Jaridians, and the entity replies that that is precisely the reason why he is not ready - he would use the Kimera teachings to destroy another race. The Jaridian is angered and growls that he will not allow her to condemn his race. As he moves forward aggressively, there is a flash of light and the Jaridian is thrown to the floor of the chamber unconscious. Lili and Liam examine him and can find no signs of life.

Sandoval receives report of an alien vessel nearby and sets his course for it. Zo'or asks how the search is proceeding, but before Sandoval can report on his findings, Zo'or tells him that he is too late and the Synod is ready to convene.

Liam faces the entity and tells her that he is part Kimera. Although it does not entitle him to special treatment, his heritage does entitle him to demand and receive answers from this ship. The entity prompts him to continue. Liam asks her to confirm that the Kimera were celestial anthropologists and that the knowledge contained in this repository was accumulated during thousands of centuries of studying species across the galaxies. He asks her if the Kimera philosophy is the same as that for all anthropologists, never to interfere with the development of any species. The entity confirms this. He asks her if it is true that every being is unique, and therefore able to impact the evolution of the species, and she confirms this also. Looking down at the Jaridian, Liam charges accuses the entity and the ship with violating the Kimera directive, with interfering with the development of species by luring them to the ship and killing them. There are signs of life from the Jaridian and Lili tells Liam that the Jaridian isn't dead. Liam continues, telling the entity that the Kimera would never have killed in their studies, but that the ship is killing and the only explanation is that its programming has been damaged. The entity closes its eyes for a moment and tells Liam that he is correct. She tells him apologetically that she will begin repairs at once. Liam tells her that is not sufficient, since her programming could become damaged again and intrinsic flaws in her programming prevent her from realizing that damage has occurred. He tells her that if the ship kills again, it will destroy everything the Kimera stood for. The entity cannot find fault with Liam's argument. When he tells her that the ship has only one option, she agrees and gives them only four minutes to depart the ship before it destroys itself. An alarm goes off and she tells them that the chambers have been deactivated and the self destruct sequence commenced. Detonation will occur in 3 minutes and 45 seconds. Liam and Lili help the Jaridian to his feet, and as he exclaims aloud about finally having the honourable death he deserves, Liam says, "Not just yet." They race for the area where the shuttles are parked.

On the mother ship the Synod has convened. One member asks Zo'or if he has any defence to the charges made by Da'an. Zo'or addresses the Synod and says that the Taelons are fighting for the life of their species and that every decision he has made is in furtherance of that imperative. In his turn, Da'an addresses the Synod and says that Zo'or violated a clear directive from the Synod to avoid any interaction between humanity and the Jaridians. Zo'or says that the knowledge gained by studying the Jaridian outweighed the risk of exposing him to humanity. Da'an replies that it was not Zo'or's decision to make and that he was serving his own interests not the interests of the Commonality. Zo'or speaks imperiously to the Synod and tells them that he was named leader of the Synod because he knows exactly where he is leading the Taelons. He is not afraid to make the difficult decisions and he challenges any member of the Synod to state that he has acted improperly. Da'an's is the only voice raised in reply. He states that Zo'or betrayed the spirit of the Commonality and demands that he step down. The other Synod members are silent and Zo'or is smug when he says that Da'an is the only one to challenge him, and as leader of the Synod, he declares the meeting is over. Zo'or looks at Da'an and the threat in his voice is implicit when he says that he will no longer tolerate opposition.

Liam, Lili and the Jaridian race back to the shuttles, evading explosions in the corridors which have already begun as the destruction sequence builds up. Lili jumps into Liam's shuttle and prepares for take off as Liam assists the Jaridian to seat himself in the other shuttle. Liam warns the Jaridian that he has only one chance at getting home because the ID drives on the shuttle will only engage once before they incinerate. The Jaridian doesn't understand why Liam saved him and Liam tells him that he owed him one. The Jaridian tells Liam that nevertheless he will kill Liam when the Jaridians come to earth if Liam opposes him. Liam simply smiles and tells the Jaridian, "Not if I kill you first." They shake hands and Liam wishes the Jaridian a safe journey. Liam heads quickly back to the other shuttle where Lili is waiting for him. The onboard computer indicates that only fifteen seconds remain until the Kimera ship self destructs. Liam climbs in and the shuttle departs rapidly. Only one shuttle is seen departing the Kimera ship so we don't know whether the Jaridian actually escaped. As their shuttle accelerates away from the exploding Kimera ship, Lili asks Liam if he thinks the Jaridian made it and Liam says that he hopes so.

From his shuttle Sandoval makes contact with Liam and Lili and asks them about the whereabouts of the Jaridian. Liam tells Sandoval that they were prisoners on an unidentified alien craft and that the Jaridian was killed in a blast when the ship exploded. Sandoval asks Liam if he is certain about the Jaridian's death. Liam interrupts him to say caustically that he and Lili sustained only minor injuries and to thank Sandoval for his concern.

Later at Resistance Headquarters Augur says that if the Jaridian actually entered the coordinates for his destination, he (Augur) should be able to track it. Lili is impressed that Augur can track any shuttle communication. When the Jaridian's programmed destination comes up on Augur's screen, Augur grimaces because he doesn't recognize it and asks if anyone knows where it is. Liam smiles and says, "His home."