The first scene takes place at night in New South Wales, Australia. What appears to be a glowing meteorite hurtles out of the sky and lands on earth. A scientist who is working nearby sees the landing and drives to the scene of the landing. When he arrives, he discovers that the object which landed is a probe of some kind and is not a meteorite at all. He tries to obtain data readings to establish what the object is, but when he touches it, a blast of energy is emitted which hurls him backward, away from the probe.

At dawn the next morning, the scientist is still unconscious and is laying exactly where he was thrown by the blast from the probe. The probe has changed its physical configuration and has sprouted three appendages resembling antennae, which extend outward and upward. A pulsating beam of light emanates from the centre of the probe.

On the mother ship Sandoval and Lili have been summoned by Zo'or, who inquires if Sandoval's strike team is ready. Sandoval reports that on his command, Companion forces world wide will engage simultaneously. He is visibly perplexed and tells Zo'or that he would be more effective if he were fully briefed on what is happening. During their discussion, it is obvious that Zo'or is suffering from an illness of some kind. He blushes violently, then begins to collapse. Sandoval and Lili move forward to steady him, but he recovers, recoiling from physical contact with Sandoval and Lili, and pushes them away with an outraged look. Zo'or lurches slowly and painfully to his chair, seats himself and tells Sandoval to give the command.

In the Flat Planet Café Augur and Maiya are conversing just before the café closes for the evening. Maiya is putting away the bar equipment and glasses. At the bar Augur is musing aloud about what his father would say about him now. He tells Maiya that the only piece of land his father ever owned is the plot he is buried in, and he brags to Maiya that now he owns an entire square block of the nation's capital. Maiya, who is puzzled by Augur's words and does not understand the concept of land ownership, asks Augur why he wants to own real estate. Augur tells her that it is so he can leave something behind when he dies. Maiya is dismissive and replies that in her world, when her people die, all they leave behind is their body for the crows to eat. Augur tells her that she sounds like his father, but that in his father's case, there was nothing left for crows to pick on except for a few charred bones. He tells her that his father died in a church explosion, trying to get a bunch of sharecroppers out to vote for something they would never have. There is bitterness in Augur's voice. When Maiya asks who he will leave his assets to, he tells her that if she plays her cards right, it could be her.

A Taelon strike team enters the cafe, with Lili and Sandoval following behind them. Sandoval begins by saying "Taelon Security. You're all being detained for questioning on suspicion of crimes committed against the --------." His voice trails off as he recognizes Maiya among the people at the Flat Planet Café; he stops for a moment, then finishes his sentence, "Companions". Maiya leaves the café escorted by a member of the security team. As Augur is also being escorted out, he asks Lili what's going on, but she tells him she doesn't know anything and pushes him out. After they leave, Sandoval angrily asks Lili about Maiya, saying that Lili had told him Maiya was in the Peruvian jungle. Lili retorts that she told Sandoval that Maiya could be in the jungles of Peru, or the streets of Bangkok, or San Francisco, or Tipicanoo for that matter. Sandoval, still angry, tells Lili that for an ex-marine Captain, her reconnaissance skills are sadly lacking. Lili, infuriated, tells Sandoval that Maiya is a cultural anthropologist and asks him what he expects. Sandoval loses his self control. He seizes Lili's arm for a moment, then releases her and tells her savagely that what he expects from her is the same loyalty she gave Boone.

Liam confronts Da'an and demands to know if it is true that Zo'or is randomly pulling innocent citizens off the street and executing them on the spot. Da'an is obviously unwell, but attempts to reason with Liam, telling him that the people taken are not being executed. Liam is in no mood to reason and retorts that it is not what he has heard. The irritated Da'an asks Liam if he now trusts idle speculation, rather than his (Da'an's) words. Liam demands an explanation for what is happening. Da'an states that there has been a rupture in the Commonality and that utilizing the mental energy of human beings is the only remedy available to the Commonality until the rupture is repaired. Liam is still angry and asks Da'an if he will stand idly by and do nothing while Zo'or just grabs people off the street. Da'an counters by asking Liam if he would prefer that the Taelons allow themselves to revert to their (Atavus) primitive state. Liam's words in parting are that he will ask Augur and Maiya that question, if they survive.

Lili and Sandoval are together and are watching those who were abducted from the Flat Planet Café. Lili asks Sandoval when this become a police state, and says they don't have the authority to grab innocent people off the street on the suspicion that they're Liberation members. Sandoval points Augur out and says "Innocent? Observe the walking neon sign with the ponytail, Captain. He's an escaped convict from Russia." Lili replies that the Russians should be allowed to deal with him. She asks Sandoval what the girl and the others have done, but Sandoval doesn't answer her and is staring at Maiya. At this point it becomes apparent to Lili that Sandoval doesn't have a clue what is going on. A bright light is trained on the prisoners, who hold their hands to their heads and begin to scream in pain. As Sandoval and Lili look on, everyone falls to the ground unconscious. Zo'or makes his entrance, ordering Sandoval to collect the unconscious prisoners and convey them to the laboratory. Sandoval who is very agitated, looks down at Maiya, and asks if the prisoners are dead. Zo'or says that they are not quite dead.

The unconscious prisoners have been placed on gurneys in the laboratory. Sandoval and Lili are looking down at them and Sandoval asks Lili why she lied to him about the whereabouts of Maiya (Isobel Martinez). Lili goes on the defensive and berates Sandoval for calling her a liar. Then she cautions Sandoval that if he continues with his obsession, he will endanger his position with the Companions.

Zo'or enters the room and approaches Sandoval and Lili. Lili falls silent. Zo'or inquires whether they have found the source of the rupture, and Sandoval tells him they have not. Zo'or asks if they understand the urgency of the situation. Sandoval tells him that he understands that the Commonality, the spiritual nexus that links the consciousness of all Taelons, has been ruptured, and that if that rupture isn't repaired.... Zo'or interrupts Sandoval and tells him harshly that it will be the end of the Taelons and that they will revert to their Atavus state. Until the source of the rupture is located, the Taelons will require a secondary spiritual energy to maintain the Commonality. Sandoval asks if the unconscious people below are providing the secondary source of energy. Zo'or explains that what humanity would call a near death experience (NDE) has been created, and that by keeping the bodies in stasis, they have forced the souls out of the bodies and into a psychokinetic containment field which in turn channels the displaced spiritual energy to the Taelons, compensating for the rupture.

Sandoval is concerned about the "sleepers". Zo'or tells him that the psychokinetic field responds to the individual consciousness of each sleeper, manifesting whatever environment the soul requires. Lili understands what Zo'or is telling them and asks Zo'or if the sleepers are creating their own heaven. Zo'or tells her that is one way of putting it and explains that the length of time one can last in stasis varies with each individual, but that they will all eventually move beyond the near the NDE state and enter the condition of permanent, irretrievable death. He tells Sandoval and Lili that if such a thing occurs, the Taelons will simply replace the current group with a new group of sleepers. Lili is horrified, and Sandoval asks if there is any alternative. Zo'or replies that the only cure is to find the source of the rupture. Sandoval and Lili exit to begin work on pinpointing the source of the rupture.

Zo'or and Da'an are standing looking down at the sleepers when an alarm goes off which indicates that one sleeper has died. Da'an tells Zo'or that they (the Taelons) have never questioned whether it is justified for them to kill others so that they might live. Zo'or replies that self preservation is a concept which was taught to him by Da'an. Da'an appeals to Zo'or, saying that it is time to take stock of their actions and to determine if they have the right to sacrifice others for the survival of the Taelon race. Zo'or scornfully tells Da'an that such an attitude is the reason he will never lead the Synod. He (Da'an) was once strong enough to do what must be done, but is no longer strong enough. Da'an's misplaced allegiance to the human race has destroyed him. Da'an asks Zo'or what will happen when all the sleepers die, and Zo'or says that they will find others to take their place.

In her near death state, Maiya is in the process of creating her own version of heaven. She has recreated the day of her wedding to Jason and is discussing the ceremony with her mother. Her brother enters and Maiya is happy to see him, but she is perplexed because she knows that her brother has been dead for some time. Her mother tells her that here they exist on a plane beyond death. When her fiancee, Jason, appears, Maiya forgets her anxiety.

Meanwhile, Sandoval has been informed that one of the sleepers is dead and tells Lili that a "subject" has died. Lili goads him, asking him if he doesn't mean "people" rather than "subjects". She further asks him if his real concern isn't about the identity of the dead sleeper and whether or not it is Isobel Martinez. Sandoval's expression is guarded and he asks her if there has been any progress on the scans. Lili tells him that she has been analysing the data for hours but is unable to trace the source of the drain. As she explains her attempts to trace the location of the device causing the rupture, she suddenly realizes that they have been approaching the problem from the wrong perspective and tells Sandoval that they have been searching for the drain rather than allowing the drain itself to show them were it is situated. Sandoval asks her to be more specific. Lili explains that the rupture is drawing in all of the subatomic waves created by the Commonality, and that if they can replicate the Commonality's harmonic signature, then the subatomic waves which they are creating should be drawn to the source of the rupture.

At Resistance Headquarters under St. Michael's church, Liam is explaining to Dr. Parks that the Taelons are intentionally initiating near death experiences in the sleepers to maintain the Commonality. He tells her that he wants her to do the same thing to him. Doors, who is also present, tells Liam to go and play his games somewhere else. He is distraught because people in his movement are dying all over the world. Liam asks Doors why the hell he (Doors) thinks Liam is doing this. Of all the people in the world, Liam thought Doors would be the most receptive to his plan. He asks Doors if this isn't exactly what he wants and refers to Doors' attempt to murder him by sabotaging his shuttle. Doors remains cool and calm and asks Liam for proof. Liam asks Doors if he is going to deny his attempt to kill him (Liam), and Doors justifies the attempted murder by saying that Liam had challenged his authority. Liam argues that there is no time for this discussion. Doors is sceptical about Liam's ability to locate Augur and Maiya on the other plane. Liam explains that he has greater control over his psychic abilities than most human beings, and that once on the other side, he should be able to direct his consciousness towards Augur and Maiya and lead them back into their bodies. Dr. Park says that the whole concept is way out of her league and that she doesn't even know if what they are discussing is possible. Doors thinks they should give it a try and tells Liam that if he gets in too deep they will pull him out. Liam grins and tells Doors that with his (Doors') track record, that doesn't give him a lot of confidence.

In his own near death state (NDE), Augur is standing on the street in his childhood neighbourhood, looking around him in disbelief when his father walks up to him. Augur remembers that his father is dead and decides that he is probably also dead and in heaven. Augur's father confirms Augur's statement and invites him to come home.

Dr. Parks is loath to perform the procedure on Liam, but at the instruction of Doors, she initiates the protocol which will initiate a NDE in Liam.

Inside his NDE experience Liam reminds himself to stay focussed and in the moment and to direct his mind toward Augur and Maiya. He locates Maiya and steps into her heaven at the moment of her wedding to Jason. Liam addresses Maiya and the wedding ceremony comes to a standstill as he tries to get Maiya to remember who he is and to recognize that she is in a NDE state. He explains that they are in a psychokinetic dimension where things are only real as long as she believes in them. Liam tells Maiya that she is in a heaven of her own making and that she has travelled back to a time before the Taelons, to the most perfect day of her life, the day she married Jason. He tells her that if she stops believing , even for a moment, the scene will dissolve. Maiya wants only to stay with Jason and her people and she desperately tries to hold on to her belief, but for a moment the wedding scene wavers before her eyes and she flees from the scene, shouting, "No".

At Resistance Headquarters Doors asks Dr. Park if Liam is OK. She tells Doors that she has never seen anything like it. It is as if Liam is alive, yet not alive.

The Taelons have been unable to locate the source of the drain on the energy of the Commonality and Zo'or issues orders that the scan parameters be recalibrated, and the scans be done again.

Augur is sitting on the front porch of his home, playing chess with his father. They are discussing the past and Augur tells his father that he was stuck in the 1960's. Augur says that when he was growing up, the only colour which really mattered was green. He is angry at his father for leaving them and "fighting the good fight". Augur's father counters by asking him what he is fighting for, a piece of art, a city block, a street sign with his name on it. Augur says that they are supposed to be in his version of heaven and his father retorts that there must be something here which Augur is missing and that he needs. Augur says that he certainly isn't missing his father. They walk into the house, and as they go, Augur tells his father that he resents him for leaving him because he had to learn to do everything for himself. He knew no one else would help him.

Suddenly Augur hears Liam's voice and turns to face Liam. Liam tells Augur that it is not true and that both he and Lili will always be there for Augur. Augur stares at Liam, but does not recognize him. Liam tries to reason with Augur, telling him that this is not his father, but a memory of his father. He asks Augur if he (Augur) remembers their fight to save the world. Somewhere in the house Augur's aunt calls out that supper is ready and Augur's father turns to go in, inviting Augur to go with him. Augur turns toward his father and a voice speaks behind Liam, "Perhaps you should be less concerned with his father, than with your own." Liam turns to see an incandescent figure standing in the doorway. In a disgusted tone, he says, "Hag'el?"

On another plane, Liam and Hag'el stand face to face, clouds moving by behind them. Liam tells Ha'gel that he is not his father, but just a projection of his (Liam's) unconscious mind. Ha'gel replies that Liam's unconscious mind contains the collective memories and experiences of countless races, and that given that fact, he (Ha'gel), is more real than most. He asks Liam if it would hurt to show a little respect to the image of his father, and Liam says that it would not. Hag'el tells Liam that has the choice of remaining where he is, and that here in this place he can create a heaven in which he truly belongs. He tells Liam that on earth he (Liam) was neither man nor Companion, but something entirely different, a being at war with himself and with the world. Liam asks Ha'gel bitterly why the hell Ha'gel brought him into this world. Ha'gel regretfully tells his only son that on earth he succumbed to a biological imperative, as the last of his kind, and he asks for Liam's forgiveness. Liam bitterly says that it is the only world he knows. He asks Hag'el if he should remain trapped in this Taelon psychokinetic prison. Hag'el laughs and responds that Liam is so much more than the Taelons are and that what the Taelons create, Liam can transcend.

Meanwhile Maiya is talking with Jason, who tells her that she doesn't belong on this plane, at least not yet. She doesn't want to leave without him, but he tells her to go before it is too late.

Sandoval and Lili are in the shuttle; Sandoval has just checked with the laboratory to ensure that Maiya is still alive in the NDE state. Lili points out the location of the device which is causing the rupture and asks Sandoval if he wishes to proceed, but he is lost in thought and is unresponsive. She asks him again; he comes out of his reverie and tells her to proceed.

In the laboratory, Zo'or is informed that the remaining sleepers will not survive the night and orders another group to be rounded up.

At Resistance Headquarters, Dr. Park is not optimistic about Liam's chances of survival and wants to pull him out of his NDE state. Doors insists that Liam must be permitted to finish what he has begun and tells Dr. Parks that when that is over, she can get Liam out, "alive".

In his NDE state, Liam is shown a gateway by Ha'gel, who tells him that if he steps through it, he will transcend the physical plane and enter a vast and boundless sea of undifferentiated consciousness and matter where all are one, the Shahariath or heaven of the Kimera. Liam understands what he is seeing and tells his father that on earth quantum physicists refer to this state as the "implicate order". He tells his father that if he does as Ha'gel suggests, there will be no Kimera left. Ha'gel shrugs and replies, "Not on this plane perhaps....". Liam steps through the portal into the Shahariath. He remains visible within it, and his expression as he begins to experience this new plane is one of rapture.

Lili and Sandoval arrive in Australia and land the shuttle near the probe. They approach the probe cautiously, weapons in hand, and Sandoval tells Lili that they must get as close as possible because they will only have one shot. Sandoval lifts his arm and prepares to fire his skrill, but is thrown to the ground by a blast from the probe, then surrounded by a force field. Because of the force field, Lili is unable to reach him, and Sandoval cannot move. He orders Lili to leave as there is nothing she can do for him. She turns and rushes back to the shuttle.

Liam is still lost in his experience of the Shahariath when Maiya and Augur appear and implore him to return to the real world with them. He is deep within his experience of the Kimera heaven and reluctant to leave it. Maiya shouts at him that he cannot throw his life away, that he made them see the truth and that he must now see it for himself.

In the laboratory Liam's life signs exhibit a flat line and Dr. Parks says they're losing him. Doors orders her to pull Liam out, and she attempts to do so, but is unable to revive him and whispers, "He's gone."

Back in the shuttle, Lili, isolates the frequency of the Commonality on her global and adjusts it. Then she leaves the shuttle with a package in her hand.

Augur is pleading with Liam, telling him that they both recreated their fathers because their father are the strongest influence in their lives. His image is beginning to waver. In the laboratory, Augur's vital signs are weakening, and it is predicted that he won't last much longer.

Augur tells Liam that he hates to rush things, but that they are short on time. Liam asks him why he should go back to a world of pain, when here he can have Nirvana. It is Maiya who finally manages to get through to Liam, telling him that there is no challenge in being pure energy, that there is no danger, or passion, no anger or sorrow, no love. She tells him that for all his pain, being human is the greatest gift there is, and that the heaven he is looking for is back on earth. Liam steps back through the gateway, telling Ha'gel that before he is ready to know the secrets of the universe, he needs to know himself.

Lili uses her global to distract the probe and lower the force field. She checks to ensure that Sandoval is all right, then arms an explosive device taken from her pack and places it in the ground close to the probe.

Liam points out a dimensional gateway to Augur and Maiya which will take them back to their bodies. They are unable to see the doorway, but Liam tells them to trust him, that it is there and that they can step through it. Augur steps through first. Maiya pauses and asks Liam about the other sleepers. Liam replies that if she takes out the Taelon NDE machine at the laboratory, they should all be fine. Maiya steps through the gateway, but Liam remains behind for a moment. He looks at his father. Ha'gel merely smiles and makes a parting gesture.

In Resistance Headquarters, a grieving Dr. Park closes Liam's eyes for the last time. Doors, who also appears to be grief stricken, is seen with his head bowed.

In the Taelon laboratory Maiya regains consciousness, sits up, and awakens Augur, who warns the lab technicians to stay out of his way, but they are too astonished to make a move of any kind. When all the sleepers have been awakened, they leave the lab together.

Zo'or condemns the sleepers saying that they have doomed the Companions and their own foolish race as well. Da'an tells him that if this is to be the end of the Taelons, at least they will be able to face it with their dignity intact.

In the shuttle, Lili is preparing to make a speedy departure and Sandoval asks her how much time they have. She tells him that there isn't enough time to say their prayers. As the shuttle lifts off, there is a violent explosion and the probe is destroyed.

Da'an is the first to sense the destruction of the probe, the repair of the rupture and the healing of the Commonality. He tells Zo'or, who experiences it himself a moment later.

Sandoval is in touch with Zo'or and Da'an on the mother ship and reports to Lili that the drain on the Commonality has ceased. He commends Lili on her good work. She inquires about the status of the sleepers and Sandoval tells her that they are awake and free. Lili is astonished and asks him if it was a gesture of mercy from Zo'or. Sandoval tells her thoughtfully that Isabel and her friends freed themselves and escaped. Lili says acidly that she should have known.

Liam's body is still in the laboratory and Doors and Dr. Park are mourning Liam when the ebullient Augur enters and asks where Liam is. They tell him that Liam is gone and show him where Liam's body is. Augur is distraught and accuses Doors of killing Liam. He cannot be dissuaded from his conviction that Doors murdered Liam. Suddenly a voice says, "No"! They all turn as Liam sits up and rather groggily tells Augur that Doors did not try to kill him. Augur runs to Liam and picks him up, lifting him right off the floor and laughingly saying, "Who says you don't have a flair for the dramatic!" Liam replies that he had a pretty good teacher. Dr. Park demands a hug and as she puts her arms around Liam, Jonathan Doors offers his hand to Liam to shake in a gesture of truce.

In the final scene, Maiya has returned to the Flat Planet Café and is working at the bar. She tells Augur that it will take a lot more than her recent experience to rattle her. She looks across the bar at Sandoval and asks him what he will have. He replies, "That's up to you."