The opening scene takes place in a laboratory on the mother ship. An alien in restraints lies on an examining table. Agent Sandoval and a human scientist are standing nearby. The scientist tells Sandoval that everything is ready. Sandoval issues instructions that he is to be informed as soon as the extraction is complete.

In another location on the mother ship, Zo'or and Da'an are talking. Zo'or believes that no matter how he rationalizes his beliefs, Da'an is more like himself than he will admit. Da'an denies it and says that unlike Zo'or, he is not trying to biologically engineer the human species. He is attempting to accelerate human evolution along its natural course; but he is not trying to alter it altogether. Liam enters the room where the conversation is taking place as Zo'or points out that accelerating human evolution is altering it. He defies Da'an to tell him how their methodologies differ. Da'an believes that the major difference is his respect for humanity and his wish to accelerate its evolution so that both Taelons and humanity can merge and create a new race capable of defeating the Jaridians.

In the lab, the scientist, Dr. Bellamy takes a blood sample from the alien's hand. A security guard tells him that the alien must be returned to stasis immediately because the security risks are too great. Dr. Bellamy tells the guard the guard that the subject will be returned to stasis when he is satisfied that he has the samples he needs.

Zo'or and Da'an ae continuing their conversation when Sandoval enters. Zo'or is the last of his kind, the last Taelon to be born in a thousand years, and he refuses to allow Da'an to contaminate the Taelon gene pool with such barbaric specimens as humanity. Da'an believes that the Taelons are a dying race, and that joining with humanity is the only way in which both races will reach the next level of evolution. Liam suddenly has a vision of what is occurring in the lab.

The alien (who is a Jaridian) escapes from his restraints, rises from the examination table and battles with the guards. He raises his hand, the palm facing outward in the classic Sha'karava stance.

Meanwhile Sandoval is attempting to contact Dr. Bellamy in the lab, but nobody is answering. Sandoval looks at Zo'or who nods his head, then gives the order to flood the lab with a "stun" pattern. When the report comes back that all life forms in the lab are unconscious, he leaves the room to check.

Zo'or and Da'an continue to talk as if nothing has happened. Da'an announces loftily that the Synod will continue to endorse his experiments in human evolution and turns to go, but he turns around again when Zo'or advises him that the approval of the Synod will be withdrawn if he (Zo'or) has anything to do with it. Da'an leaves accompanied by Liam.

Sandoval makes his way to the laboratory where the Jaridian was being held and looks around. There is a large hole in the wall of the lab surrounded by scorch marks. He gives instructions to return the Jaridian to stasis, and asks Dr. Bellamy if he was successful in extracting the samples which he required and will be able to isolate the Jaridian's DNA for use in Da'an's experiments.

Dr. Bellamy is shaken by his ordeal and no longer sure about the experiment and its consequences. Sandoval orders him to carry out the experiment precisely as Zo'or wishes and leaves the lab. Dr. Bellamy, who is visibly apprehensive, remains behind.

In another lab, Dr. Bellamy takes the vial containing the Jaridian's sample and adds its contents to several other vials which also contain a solution of some kind. He looks around to make sure that he is alone in the laboratory and finishes what he is doing. When he has completed his task, he contacts Sandoval and tells him that everything is in readiness.

On the bridge, Sandoval looks at Zo'or and nods, almost imperceptibly. Zo'or's response is a pleased expression.

On earth, a conference is taking place at the Taelon/Human Genetic Research Facility in Dallas, Texas. Dr. Belman is explaining to a large group of physicians and geneticists that today humanity stands on the threshold of a remarkable breakthrough in medicine, thanks to the support of Da'an. Human and Taelon technology have been combined in a technique which may allow humans to heal themselves in ways never before imagined. She introduces two members of her research team, her daughter, Dr. Joyce Belman, and Dr. Peter Bellamy (the scientist from the laboratory). Joyce addresses the audience and tells them that the Taelon race is much further along the evolutionary ladder than humanity is. One effect of their advanced evolution is that Taelons can psychologically manipulate organic matter.

A subject is brought in on a stretcher and Joyce introduces him as Max, an ape who was discovered in a poacher's trap that morning and liberated. Max's internal organs have been terribly damaged by his ordeal, and this is illustrated on a screen at the back of the stage. Max's only chance of survival lies in the new technique which has been developed. Joyce tells the audience that the key to the success of the healing technique is the subject's desire to heal themselves, and that an ape has the requisite intelligence to focus his mind on healing. She injects Max with a syringe of solution containing an evolutionary accelerant derived from Taelon DNA. It will propel Max along the evolutionary ladder to a level where he can heal himself. The audience watches in rapt silence as Max heals himself and applaud. One of the audience asks when the team will be ready to test the new drug on a human being. Dr. Belman replies that they are not yet ready, but that negotiations are in progress between Da'an and President Thompson.

President Thompson and Joshua Doors are discussing the experiments on their way to the Presidential limousine. Joshua believes the experiments and their possible consequences are even broader than the cloning issue back in the 1990's. He warns the President that until there is adequate accountability by the Taelons, the only option is to place the genetic research in abeyance. Thompson fully supports the genetic research and plans to expand the scope of the experiments. Thompson attempts to put Joshua in his place, telling Joshua that he is only there to serve him. Joshua is adamant about the lack of safeguards on the genetic research project. He dismisses the President's statement that he (Joshua) has no authority in the matter in spite of being Secretary of Taelon Relations and having authority over anything involving the Taelons. He also accuses Thompson of thinking him stupid and says Thompson needs both him and his trust fund because the American people don't think Thompson himself has the courage to stand up to the Taelons. Thompson gets into his limo saying that he doesn't have to tolerate this. Joshua threatens to go to the public with the truth about the genetic experiments. Thompson remarks that Joshua doesn't have a case or a constituency and that the only public voice he has is the one Thompson gave him. Joshua hands Thompson his resignation effective immediately, thanks Thompson for giving him a public voice and tells Thompson that it will help him in his next job as campaign manager for the man running against him for the office of President.

When the conference is over, Liam introduces himself to Dr. Joyce Belman while her mother, Dr. Julianne Belman, talks with people who were in the audience. Joyce feels that her mother's "campaigning" for funds demeans the scientific objectives of the research. Liam tells Joyce that it is crucial to obtain funding for the program, and that the only thing which concerns her mother is getting the best people for the job. Joyce says she doubts her mother would agree she has the best team, because although she (Joyce) is the most qualified scientist in the area of the project, her mother tried to prevent her from being on the team.

In the laboratory Max is returned to his cage and fed. He begins to behave in frenzied fashion, screaming and flailing about in his cage.

Da'an informs Dr. Belman Sr. that Zo'or is trying to terminate her project. With the threat of the Jaridian invasion, Zo'or's idea of bioengineering humanity as soldier is favoured by the Synod and leaders on earth. Dr. Belman says they have already made great progress and Da'an says that is not enough, the only way to prevent the project from being terminated is to test it on humans and prove it is effective. Dr. Belman refuses and says that it would be scientifically irresponsible to do so. Da'an tells Dr. belman that her daughter Joyce disagrees with her assessment, but Dr. Belman says that Joyce is wrong. Apparently Joyce got onto her mother's team only because Da'an insisted on it. Joyce is a leader in the field in which her mother is working and Da'an won't allow her suggestions to be discounted. Dr. Belman angrily turns to leave, stating that if Da'an wants to replace her as project leader, he can do so, but there will be no human testing until she gives the order.

In the laboratory, Dr. Belman confronts Joyce about approaching Da'an behind her back. Joyce says she thinks they are ready for human testing, and she merely gave Da'an her honest assessment of the situation. Dr. Belman insists that Joyce is wrong and Joyce tells her mother that she expected this because she didn't want her on the project in the first place. Dr. Belman demands what Joyce is trying to prove, and Joyce bitterly tells her mother that she only wanted to be a part of the project for her mother's sake. Dr. Belman is speechless and leaves the lab.

One of the scientists returns to the lab to check on Max, the chimp, As he walks to the cage, its door is thrown open and the scientist is thrown clear across the room by something he cannot see. He looks up to see Max leaping at him.

In the laboratory, Joyce thoughtfully removes a vial containing genetic solution from a lab cupboard and looks at it, the same vial which Dr. Bellamy was holding earlier. She carefully removes her jacket and make an incision in her arm using a scalpel.

A security guard goes to the lab where Max was being kept and finds it has been completely trashed. He contacts Dr. Bellamy at once, then draws his weapon and searches for the scientist. Max hides under a table and watches unseen while the guard searches.

In the other lab, Joyce injects herself with the genetic solution and waits for it to begin to work.

The guard locates the unconscious scientist, but is ambushed by the frenzied chimp. Dr. Bellamy and Sandoval enter the lab together and Sandoval stuns Max with his skrill, causing both Max and the guard to collapse. Dr. Bellamy begs Sandoval to let him destroy the accelerate solution because it is too volatile, but Zo'or will not allow the accelerate destroyed until the Synod cancels Da'an's project. Sandoval orders Dr. Bellamy to get Max back in his cage and leaves.

Joyce looks at the incision in her arm and watches it wonderingly as the incision closes and her arm heals up. She suddenly cries out and bends over clutching herself in severe pain. For a moment, she seems to be surrounded by a nimbus of light, which moves away from her and dissipates into the air around her.

Later, Joyce stand in a park listening to the music which is emanating from a nearby band shell. Liam arrives on the scene and tells her she looks stunning. He asks her if she plays an instrument, and she tells him that she did, but gave it up long ago. Liam asks her if she has ever been in this park before and she tells him that it was a special place where she and her mother used to come when she was growing up. He asks her why she wanted to meet him here. A nimbus appears briefly around Joyce, and the horrified Liam, seeing it, asks her what she had done. Joyce tells Liam that she injected herself with the serum and that it has already taken her far beyond anything anyone ever imagined. She's growing every second, learning, changing, evolving, and her ability to manipulate matter isn't limited to just healing wounds - there are no limits to what she can do. Liam tells her that the serum isn't stable. Joyce interrupts him and tells him to look at the flute which was left on a chair in the band shell. Alone and without a musician, the flute is playing the first piece of music Joyce's mother taught her when she was a child. When Liam moves to use his global, Joyce tells him not to bother, that her mother will be calling him any second now. She holds out her hand and the global moves into it. When it beeps, Joyce answers and tells her surprised mother that she should not worry, that Liam is with her, and she can't wait to share her news. Before Dr. Belman can say anything else, Joyce ends the transmission and walks away, hand in hand with Liam.

Joshua and Lili are watching a television newscast together. A television a newscaster reports that Joshua has resigned and that a news conference has been scheduled for later. Lili is irritated because Joshua did not tell her about his plan. They have a conversation in which it is revealed that they have been dating secretly for about two months. Joshua is curious about why their relationship is secret and speculates that it is because Sandoval would not approve. Lili tells him that she worries about his safety because of his anti-Taelon sentiments. Lili asks Joshua what his plans are and he tells her that he will be working to defeat Thompson in the next presidential race. Lili doesn't think he has a chance and Joshua tells her that there is one man who does.

Liam, Joyce and Dr. Belman are in the lab and Joyce seems to be bathed in an aura of light. Her stricken mother wants to know why she did such a thing, and Joyce assures her that she is fine and is evolving in ways they would never have imagined. She leaves briefly and Liam takes the opportunity to ask Dr. Belman if there is any way to reverse the effects of the serum. Dr. Belman tells Liam that her research has not gotten that far. She can't understand what is happening to Joyce because the serum was specifically targeted at the healing centres of the body. She decides to take a blood sample from Joyce.

Joyce tells her mother that she knows about her involvement with the Resistance, and that she can see everything which is in her mother's mind. She now knows that her mother loves her and pushed her away to protect her. Dr. Belman is flustered and tells her daughter that there will be plenty of time to talk after they have reversed the effects of the serum. Joyce tells her mother to do whatever she thinks must be done. Liam who has been watching Joyce closely, tells Dr. Belman that Joyce is merely toying with them, and Dr. Belman says she knows. She has examined the DNA from Joyce's blood sample and is puzzled by what she as found. The serum has to have both Jaridian and Taelon components to succeed and elements of Jaridian DNA were synthesized in the lab specifically for the experiment, but Joyce's blood contains other elements of Jaridian DNA. Joyce tells them that the DNA in her blood is pure Jaridian DNA. Dr. Belman and Liam realize that the serum has been deliberately contaminated and are trying to figure out how it happened when Sandoval enters and summons Joyce to the mother ship to see Zo'or.

At Resistance Headquarters, Lili, Doors and Augur are watching Joshua's press conference. He asks his audience if they want to determine their own fate, or follow President Thompson and permit the Taelons to chart the course of Human evolution. He says that he puts his own faith in humanity, and that they need a man who can stand up to the Taelons. He ells the audience that the only man who has proven that he can stand up to the Taelons is his father, Jonathan Doors. Doors is angry and tells Augur and Lili to turn off the television. Lili has been thinking about it and tells Doors that it may be the perfect time for him to emerge from hiding. When Doors confides his worries about his personal safety, Lili tells him that he will be the most visible person on the planet, covered by the press for every hour in the day. Augur says that the Taelons can't kill him with the whole world watching; he adds that they will have to wait until the cameras are turned off. Doors is not amused and walks away.

On the mother ship, Sandoval and Zo'or are questioning Joyce, and Joyce tells them that their limited intelligence make it impossible for her to explain things to them in a way they would understand. Zo'or is highly insulted by her words, but Joyce doesn't offer any further information. When she asks to return to earth, Zo'or makes the mistake of telling her that she will be returned when he decides that it is to time for her to go. She asks Zo'or if he really thinks he can keep her there. Suddenly she disappears from view, only to appear again behind Zo'or's chair. Zo'or panics and orders Sandoval to fire at her and Sandoval fires, but does not injure Joyce who actually appears to be stronger after he fires at her. Zo'or orders Sandoval to kill Joyce, but as Sandoval raises his arm to fire, she directs a blast of energy at Sandoval's skrill, incapacitating it. Sandoval collapses in pain. Zo'or orders security to come to the bridge, but tells them to stay back when Joyce asks him sweetly if he wishes to die.

Liam and Da'an are conversing and Liam tells Da'an that he cannot help Joyce unless he learns more about the evolutionary split between the Taelons and the Jaridians. Da'an tells him that when the Taelons and the Jaridians were a single race, they possessed a full compliment of evolutionary tools, but when their races segregated to evolve along separate paths, each left behind a vital evolutionary component in their DNA. Liam understands that Joyce's DNA now possesses the fully integrated evolutionary components of both species. Da'an agreed that it is so for the first time since the Taelons and Jaridians diverged, and says that Joyce is about to evolve beyond the point to where either Taelons or Jaridians can evolve separately. Liam is curious why the Taelons have not injected themselves with Jaridian DNA and Da'an tells him that the two races are no longer genetically compatible. Da'an feels that humanity is the missing link.

On the bridge of the mother ship, Joyce is musing aloud about the new world which she will create. She tells Sandoval and Zo'or that humanity is too low on the evolutionary ladder to include them in her new world. She had hoped that the Taelons were worthy, but has decided that was a mistake. When Zo'or asks her about her new world, she tells him that it is the same one he wanted to create , but didn't have the power to make real. Zo'or tries to convince her that the Taelons are on earth to help humanity destroy the Jaridians. Joyce tells Zo'or to stop wasting her time with lies because she can read his thoughts and knows his ultimate plan. She will destroy humanity and the Taelons and create a new world in her own image. With a thought, she shuts down the mother ships's systems, putting the ship on a collision course with earth. Zo'or tries to bargain with Joyce, but she tells him sweetly that he has nothing to offer her and disappears.

Elsewhere Liam tells Da'an that if the mother ship crashes into the earth, the ID drives will rupture and explode, scattering the earth across several dimensions. As he prepares to leave, Joyce appears. He pleads with her to stop what she is doing, but she couldn't care less about humanity and that he is greater than anyone else on the planet. After she cleanses the earth of humanity and Taelons, they will engender a new race together. Da'an inquires how she can call herself an evolved being when she intends to destroy two species in the interest of her own vanity. She asks Da'an how many thousands of races the Taelons have destroyed. When he replies that it was a matter of survival, she remarks that those the Taelons destroyed might not see it that way.

Sandoval has made calculations and tells Zo'or that if the conventional drives can be restored in time, they can avoid colliding with earth. The drives must be restored before the mother ship reaches a distance of 28 000 kilometres from earth. If the mother ship is any closer, the drives will not have enough power to correct the course. Zo'or asks about restoring the ID drives, but there will not be enough time. Zo'or orders everyone to work on the conventional drives and Lili volunteers to assist.

On her way to the engineering section, Lili makes contact with Augur and tells him that a power drain has damaged the ID drive and that it will take some time to get it back up and running. Augur, who is watching the mother ship descend toward earth from Resistance Headquarters tells Lili that they should focus on conventional drives. Lili says they are doing so, but that it won't help them if they aren't back online in time. She asks Augur if there is any way to jump start the ID drives to make them power up faster.

Joyce is wooing Liam with every wile at her disposal, but he is not receptive to her. He thinks (and tells her) that she is a child who has suddenly acquired all the secrets of the universe without the maturity to understand them. She threatens to force Liam to go with her, but he tells her that won't be necessary because he will go with her willingly, much to the dismay of Da'an who is watching this exchange.

At Resistance Headquarters, Doors watches a news broadcast of what is going on with the mother ship.

Sandoval is able to tell Zo'or that everything is in readiness and that they are still within range. Zo'or gives the order to engage the drives, and the ship trembles, but the drives are not strong to correct the ships's course and it continues to descend toward earth.

Joyce decides that it is time for her and Liam to leave. Before leaving, he asks her to do one thing for him, to join with him and experience all the races within him so that she will come to know them before she destroys them. They join hands and are enfolded within a nimbus of light as Da'an looks on.

Lili arrives at the ID drive unit and gets in touch with Augur, telling him to impress her with his brilliance. Augur says that if they initiate a fusion reaction within the ID drive unit, it could theoretically generate enough power to jump start the unit. The hard part will be controlling the magnitude of the reaction once it starts. If the reaction is too weak, the drive won't power up, but if the reaction is too strong, the consequences will be catastrophic. Lili wants to know what the margin for error is. Augur tells her regretfully that there is no margin for error and that they will have to hit the mark exactly. Lili is worried about controlling the reaction and Augur says that they could but that there is no time to test it. He tells Lili that he is working "in the dark", and she makes the flippant rejoinder that rumour has it he does his best work in the dark. Augur ignores it and tells her how to realign the ID drive unit.

There is only forty-five seconds left until the mother ship impacts with the earth. Lili makes the last adjustment to the ID drive unit and as Augur tells her to clear out fast, runs from the drive chamber, just making it before the reaction is initiated.

Sandoval tells Zo'or that someone has entered the ID drive deck. Zo'or replies that it is probably just a Taelon engineer who refuses to leave. Lili contacts Sandoval and tells him to activate the ID drive. Sandoval hesitates for a moment and Lili tells him to do it NOW. He does so and the mother ship goes into ID space, only seconds away from impact with the earth. Sandoval tells Zo'or with relief that the drives are operational, but they look around fearfully, both expecting Joyce to return and pop out of thin air at any moment.

Joyce's joining with Liam is over, and she steps away from him, saying in a quieter and gentler voice that she understands, that without all of those other races she has glimpsed within Liam, her own existence is meaningless. She thanks Liam for sharing himself with her, and he tells her wistfully that she now knows more about him than he knows about himself. He says that the knowledge is there inside him, but that he is unable to access it. Joyce comforts him saying that he will be able to do so when the time is right. Da'an tells Joyce that she has a great journey before her and she replies that her time on earth is not quite finished.

Joyce goes back to the laboratory where everything began, and heals Max of his mental torment. Then she whisks herself and her mother off to their special park, where once again the music they have loved is playing. Dr. Belman tells Joyce that she hasn't been there in twenty years, and Joyce replies that she herself never stopped coming here. Her mother expresses regret for "so many things". Joyce takes her mother's hands in hers and tells her that she knows everything, and that there's no reason to be sorry. She forgives her mother and tells her that she must leave now. The tearful Dr. Belman asks why Joyce has to leave, and Joyce tells her that she has come too far now and no longer belongs on this earth. She tells her mother that she loves her, then is suddenly gone in a cloud of light which disperses upward into the sky. Her mother whispers, "I love you too."

Joshua walks into his dark apartment and has just switched on a lamp when he hears a stentorian voice speak from the shadows beyond the circle of light cast by the lamp. "That's a hell of a way to say hello, after three years of silence." Jonathan Doors steps into the light.