The episode opens at the cold fusion plant owned by Doors International near Albany, New York. A group of workers watch from a catwalk as engineers in safety gear and radiation suits work below. Also on the catwalk are Joshua Doors and an agitated Ronald Sandoval. Joshua makes a comment about cold fusion being "clean unlimited energy for the new era". Sandoval is edgy and says that it won't be the case if the procedure does not begin in ninety seconds. We learn that Sandoval's orders were to have the core energy canister back on the mother ship without delay. Joshua confirms that they are about to begin cold fusion with deuterium. Sandoval is most emphatic that the engineers must recover the entire allotment.

Renee appears on the catwalk and commends Joshua, saying that he has done an amazing job. We learn that Joshua was forced to leverage Doors International "to the edge of the abyss" to get the cold fusion project up and running. Renee tells Joshua that Doors Senior (Jonathan) wrote the book on brinkmanship. Apparently the stockholders of Doors International are skeptical about the cold fusion project and are screaming for Jonathan's head, but Renee says that will change when the stockholders learn "that cold fusion converts to hot revenue". She also makes the observation that Joshua is both fulfilling his father's great visionary quest, that of unlimited energy for the whole planet forever, and creating a legacy of his own. An engineer gives Joshua the thumbs up, signaling that all is in readiness to begin the cold fusion process. Everyone is requested to clear the floor and to don protective eye wear. The supervising engineer tells Joshua that the catalyst is ready to tap into the core energy source. Joshua steps to the instrument console and begins the countdown for the initial phase generation. The chamber begins to vibrate violently; there is a blinding flash of light and an explosion. Those on the main floor and on the catwalk are thrown to the ground. Sandoval immediately dons protective gear and runs down onto the main floor to see what has happened. The engineer is shaken and says that a hundred system checks were performed before the fusion process was initiated. Renee Palmer checks the instrument console and remarks that the system has shut down due to a glitch and that everything appears to be under control. On the floor below, Sandoval has discovered the shattered remains of a portable ID portal on the main floor, but the canister of Taelon core energy has disappeared. The question is asked whether the canister imploded, but there is no evidence of that having happened. Sandoval gives the Volunteers orders to seal the building completely and to search every person and vehicle until the canister is found.

On the Mother Ship, Sandoval tells Zo'or that the co-ordinates of the portable ID portal found at the scene of the accident were erased in the explosion. Sandoval has checked every portal within five hundred miles (without success) and the interrogation net is now being widened. He expects to receive a ransom note, and thinks it is also possible that the core energy is being repackaged in small units and resold by the thieves. Zo'or, furious and barely in control of himself. He says Sandoval has theories, but no results to give him. He casually inquires about Sandoval's birthplace, and Sandoval, caught off balance, reluctantly reveals that he was born on the Pacific Rim in the Caya Islands. Zo'or viciously punches a button on the panel in his "throne" and tells Sandoval that he has just unleashed a tidal wave which will destroy the Caya Islands within ten minutes. He speaks silkily of the tidal wave as a natural calamity, and makes it clear than until he regains what is his (the canister), human blood will continue to be spilled. There is no obvious reaction from Sandoval, but the expression in his eyes make it clear that he is horrified.

At a Washington reception Renee meets Hubble who asks her whether she slept at home the previous evening. Renee replies that she spent the entire night being interrogated by Sandoval and the Volunteers about the explosion at the cold fusion plant in Albany. She asks Hubble where Liam is. Hubble tells her that Liam is on duty, and that at this moment, he is escorting the guest of honor to the reception. Liam escorts the Taelon warlord, T'Than into the reception chamber, passing through what appears to be a security scanning device at the entrance of the room. After T'Than joins the reception in progress, Liam goes immediately to a console in the corner of the room ands asks the scientist who is sitting at the console if it is really possible to scan and analyze the Taelon metabolism. We learn from her reply that Taelon core energy is to the Taelon race what blood is to humanity. In the union of Taelon and core energy, a nuclear gravitational bond is created, the scientific phenomenon which Albert Einstein had theorized and called a unified field. According to the scientist, a healthy Taelon who possesses full complement of core energy should have a full purple aura, but she has scanned the Taelon warlord and is shocked to discover that T'Than has virtually aura. at the same time that the Taelons are a dying race.

In his office at Doors International, Joshua Doors powers up his computer system and the holographic image of his father Jonathan appears on the screen. Joshua is weary and distraught after his interrogation by Sandoval. His father implores him to be strong and to hold on, telling him that they will starve "the Taelon bastards" off the planet.

On the bridge of the mother ship, a console indicates a low energy reading. Zo'or glances at it and cries out in pain.

Jonathan Doors has returned to cold fusion plant, the scene of the canister's disappearance, where he encounters his father's hologram on the monitor of the instrument console. Joshua asks his father where the canister is and pleads with Jonathan, saying that he will return the canister without anyone learning the circumstances of its disappearance. Initially, Jonathan refuses to answer his son and Joshua begs, saying that he (Joshua) will be blamed by the Taelons for the theft of the core energy. Jonathan finally admits that the canister of Taelon core energy is in ID space, traveling back and forth between a thousand ID portals at random. He tells his son that his own artificial intelligence program (AIP) is generating disinformation, and that there is nothing for Joshua to worry about. Renee enters the cold fusion plant and is bewildered to hear what she thinks is the voice of the late Jonathan Doors coming from the control area.

On the mother ship Da'an and T'Than walk down a corridor together. Da'an is assisting T'Than because the Taelon warlord is stooped and in great pain and it is obvious that he is dying. He tells Da'an that he had always expected that he would live to see a time when Taelon race had been successful in their battle with the Jaridians and the earth was populated with Taelon offspring. He speaks of Zo'or's crimes, exhorting Da'an to be vigilant and to transcend the paternal bond with Zo'or. Then, taking a vial from Da'an he steps into a large chamber in which vast numbers of Taelons lie, row upon row, either dead or sleeping.

Liam and Renee visit Street's mobile home in the fringes and sit outside, discussing recent events. At Liam's request, Street has checked all the available logs and can find no record of any Taelon obituaries. They speculate about whether Taelons are simply skin suits filled with core energy and wonder whether Taelons actually die or if they just fade away. Liam asks Street to return to Augur's lair and perform a head count of Taelons, cross referencing the results with Augur's own Taelon database; he feels that the numbers of Taelons on earth must be declining since their core energy is running out. Street makes a comment about being time for her to move on anyway, and Liam responds with a joke about her selling bootleg passes. Renee has been very troubled since her visit to the Cold fusion plant and hearing the voice of Jonathan Doors. She chooses this moment to ask Street if it is possible to create a software simulation of oneself with a pre-planned agenda. Street replies that it would be easy to create such an artificial intelligence program (AIP) with a digital holographic interface. Renee tells Liam and Street that she believes that Jonathan Doors is still around, and that he is guiding Joshua's steps at Doors International. They discuss the type of degree of processing power that would be required to create an AIP of Jonathan Doors and are in agreement that co-processing and a very large mainframe would be essential. Renee tells Street that Doors taped everything while he was alive and there is an excellent archive of material for use by a Jonathan Door AIP . She gives Street a password to access the Doors International databases (Madox, the name of Doors' late wife), and Street is able to access the databases, but when she breaks into the database, the stern and threatening holographic image of Jonathan Doors appears on her screen, warning her away from the information. Street is startled and says "freak alert".

On the mother ship, T'Than has entered the chamber where row upon row of Taelons lie in suspended animation and has lain down on a vacant platform. He is about to drift into stasis when the door opens and Zo'or enters the room with an evil expression, saying that he has dreamed of this moment for a thousand years, that T'Than will never return from stasis, for Zo'or has discovered the human maxim of survival of the fittest and intends to survive, whatever the cost. Zo'or reaches out and kills T'Than with a touch. At the moment of the Taelon warlord's death a bolt of core energy is released which rejuvenates Zo'or, who appears to have become a vampire of sorts, preying on his own kind.

Joshua Doors is in his office at Doors International, conversing with his father's holographic image, and is compelled to shut off the holographic image of his father when Renee enters the office. She asks Joshua about his father "still being around" and when Joshua treats her question as a joke, tells him to stop pretending, that Jonathan paid her a visit the previous evening. She tells Joshua that she now believes the cold fusion project was a just a charade engineered to steal the Taelon core energy. She berates Joshua, inferring that he would never have done such a thing on his own, but that he is haunted by guilt about his father's death. She also says that "Cyber Dad" conveniently popped up just in time to give him (Joshua) a chance at redemption. Joshua replies that Renee doesn't know what she is talking about. He has decided to sell his own stock in Doors International to the republic of Rostok and Federov. Renee is scandalized, saying that Chairman Federov is a criminal. Renee asks Joshua to think things over, and as she leaves he says cheerfully, "Oh, by the way, you're fired."

As Joshua leaves his office, the holographic image of Doors appears and says that he (Joshua) can't mean what he said, that he must be bluffing. Joshua tells his father's holographic image that he is not bluffing about selling his shares and leaves. On the way out, he encounters his father's image everywhere, in the windows, on the wall of the building, on a canopy above the entrance, and even on the global that he is wearing on his wrist. Joshua removes his global (still displaying his father's image), throws it on the pavement and flees.

Liam and Street discuss events in Augur's old lair under St. Michael's church. They have superimposed the present image of the mother ship on an image taken some time previously and they notice immediately that the mother ship is shrinking in size. The mother ship is an organic creation and is maintained by core energy. An infra-red scan of the mother ship indicates that while its engineering section shows normal core energy levels, many other areas have been shut down or contain little or no core energy. It appears that the Taelons are shutting down areas of the mother ship which are not completely necessary for operations. The scan also indicates the presence of a hidden room, the existence of which Liam was unaware, a chamber in which "little blocks of core energy appear to be lined up like dominos". Liam leaves to explore the mother ship and locate the secret chamber.

On the mother ship Liam finds the hidden chamber and enters it. He locates the platform containing T'Than and is examining it closely when Da'an enters the chamber and is outraged to find him there, telling Liam that he has no business there, that his presence is a violation and the chamber is sacrosanct. Liam replies that as a companion protector, he has the right and a responsibility to be there, that Taelons are dying. Da'an tells Liam that the room is a stasis chamber, that it contains the physical forms of those Taelons who have reached critical level, and that they will be revived when it is possible to "reconstitute" them. Liam replies that Taelons really are dying. He shows Da'an the small energy pack attached to T'Than's resting place which is designed to create the illusion that T'Than is still alive, and he tells Da'an that the Taelon warlord is truly dead.

Outside the cold fusion Plant Sandoval finds Joshua's global lying on the pavement with the image of Jonathan Doors still displayed on its face.

At Doors International, Renee enters Joshua Doors office (formerly that of his father) and speaks aloud to the empty room, saying jocularly that she knows Jonathan is there. When Doors finally manifests on the computer monitor, she tells him that he is in the wrong dimension. Doors replies that he may, perhaps, can be considered dead in the physical sense. Renee accuses Jonathan of using Joshua as a pawn in his own game. Doors replies that he intends to assist his son in reaching his full potential. Renee asks Jonathan to let Joshua go, saying that he will let go if he really loves Joshua. After she leaves, Jonathan says, "I can't ."

At Augur's former lair, Liam, Renee and Street are discussing Joshua and the AIP which is Jonathan Doors ("Cyber Dad"). They are now aware that Joshua has been getting direction from his father in running Doors International, and they are speculating about why Joshua would choose to do so. Renee believes that Joshua's compliance is motivated by love and guilt. Liam asks Street if she can manufacture a virus to take out the cyber Jonathan Doors and she reacts angrily saying that she doesn't do viruses and asking him if she "has [CONTROL-ALT-DEL] tattooed on her forehead." She tells them that the cyber Jonathan program IS a virus. At that moment an media wide announcement commences and the implacable face of Jonathan Doors fills the screen. He tells the Taelons that the time has come to confess their seven cardinal sins, the sins of abduction, torture, murder, experimentation, mind control, financial plunder and political subterfuge. He orders them to disband the Volunteers, to vacate their embassies and to leave the solar system at once, promising to send them core energy in small increments so that they can continue to live. Jonathan warns them to take no retribution against his company, his employees or his son, Joshua. He takes upon himself the blame for theft of the core energy canister.

On the mother ship, Zo'or watches the Doors announcement and orders Sandoval and the Volunteers to bring him Joshua Doors, alive.

The Volunteers search for Joshua throughout the Doors International complex, but they are unable to find him. Liam and Renee are watching outside the building and note with satisfaction that Joshua has not been apprehended. They are wondering where he is, then look up and see him sitting on the edge of the roof in a pensive and abstracted frame of mind. When they reach his side, he tells them that it is quiet and peaceful there on the roof, that his father is everywhere, and that the roof is the only place where he is free from his father's presence. They persuade him to accompany them to a place of safety.

At Augur's Lair, Liam, Renee, Street and Joshua discuss "Cyber Dad". Joshua admits that the cold fusion plant was a plot to get the Taelon core energy off the mother ship. He tells Liam and Renee that the canister is somewhere in ID space shuttling between portals, constantly on the move and at random. Joshua speaks of his father as if Jonathan is still alive. Liam and Renee tell him that Jonathan is dead, and Joshua asks them to "define dead". Liam asks Street for some computer cyanide to banish Jonathan, and she indicates she has already created something to exorcise the AIP, then gives Joshua a disk containing the program she has created. Jonathan's AIP is deriving its power from a monster mainframe and they ask Joshua for the location of that mainframe. Joshua looks down at the disk Street has given him and says he cannot kill his father again. Street tells Joshua that he will merely be neutralizing his father, not killing him. Liam tells Joshua that it is time to cut the umbilical cord and that if Taelons begin to die, humans will also die.

At Doors International, Joshua inserts Street's disk into the computer to begin the process of arresting his father's AIP program. Jonathan appears, this time as a full size hologram and begs his son not to continue, accusing Joshua of betraying him after he sacrificed his own life for Joshua. Joshua replies that he has been haunted enough. Jonathan tells Joshua that his AIP is not without imperfections perfect, but that his human motives were not without merit and that he loves his son (Joshua). Realizing that events have progressed beyond his control, Jonathan pleads that he is only human, then instructs the computer to abort his program and purge his files. The holographic image wavers and is gone.

Liam contacts Street who is still in Augur's lair to tell him that Cyber Jonathan destroyed himself. Street says that Jonathan is dead, but not forgotten and that his AIP program is running secretly on every Info Loop computer in the world - to get rid of Cyber Jonathan it would be necessary to destroy every one. Joshua Doors has disappeared and locating the canister without him will be difficult, but they decide to flood the portal system, leaving a single portal open. All stationary and portable ID portals are frozen, leaving open a single portable ID portal outside Albany, New York near the cold fusion plant owned by Doors International.

Liam and Renee arrive at the cold fusion plant and discover Joshua Doors preparing to initiate a fusion process. He complements them on freezing the portal system. Liam asks Joshua to shut the system down and volunteers to take the core energy canister back to the mother ship, but Joshua declines, saying that he is carrying out his father's vision and that it is his choice. At this moment Sandoval and a team of Volunteers arrive. To cover up the real reason for his presence, Liam draws his weapon and orders Joshua to stop, just as Sandoval shouts at Joshua to shut down the reactor. Sandoval is too late - Joshua has already begun the process, the canister explodes in an massive outward burst of energy and is gone.

On the mother ship, Zo'or sees the violent burst of energy rising from the planet's surface and cries out, "No", in anguish.

At the cold fusion plant, Sandoval and the Volunteers take Joshua into captivity and Sandoval tells Joshua that he threw everything away and his future is now dim and painful. Joshua replies that it is his path and his pain. He is strangely calm and asks for a favor from Sandoval, who allows him to speak with Liam and Renee. Joshua's words to them make it clear that he is at peace, comfortable with his actions, and ready to bear the consequences for what he has done. Joshua tells them that he knows who he is and who he is not and that he can live and die with that. He assures Liam and Renee that he is not a martyr.

On the mother ship, Da'an and Zo'or meet in the Stasis Room. Da'an denounces Zo'or for his unspeakable crimes against humanity and his fellow Taelons, especially his murder of T'Than. Zo'or is wearing T'Than's ceremonial sash, and Da'an says that he is not fit to do so, that the act is a travesty. He tells Zo'or that it is his duty to inform the Synod of Zo'or's crimes. Zo'or is defiant and taunts Da'an, daring him to tell the Synod what he has done. Da'an tells Zo'or that the late T'Than had told him to be vigilant and to transcend the parental bond between himself and Zo'or. As the episode closes, Da'an takes Zo'or's face between his hands, and admits that he cannot betray his own child and Zo'or expression as Da'an speaks is smug. As the two Taelons touch, there is a burst of core energy between them.