The opening scene takes place at Renee Palmer's apartment building. A masked intruder climbs over the balcony. As the intruder approaches the entrance to Renee's apartment from the sun deck, an automated voice states that the security system is armed and that there is a security breach in Area 5. The intruder sprays something on the security panel at the entrance. The automated voice now identifies the intruder as Renee and permits her to enter the apartment. The intruder goes down the stairs to Renee's study, dons optical surveillance apparatus, and places a disk device on Renee's desk.

While the intruder is still inside her apartment, Renee Palmer returns and is immediately notified by the automated voice that her security system has been disarmed. She pulls out her weapon an pursues the burglar through her apartment. A brief struggle ensues in which Renee is knocked to the ground. The intruder jumps off the balcony into a portable ID portal on the side of the building and vanishes.

Renee meets Liam on the promenade outside her office building and describes the events at her apartment. There was no sign of forced entry and her security system did not appear to have been tampered with. The intruder entered from the sun deck which Renee shares with three other apartments and Renee tells Liam that her entrance from the sun deck has the same optical scanning device as her front door, an optical scanning device which reads Renee's DNA from the tear fluid in her eye. Renee tells Liam that when her security system is armed, the whole apartment shifts one quarter of a degree into four dimensions, and that one cannot simply break in because the apartment is not there. Liam remarks that the system could not be fooled with a blood sample or a skin swab, because it only responds to living DNA. Because the intruder used a portable Taelon ID portal to escape, Renee thinks the Taelons are behind the break in. Liam tells her that there are a lot of pirate ID portals available on the black market these days, and the intruder may not have been a Taelon operative at all. He is curious about what the intruder was looking for. Renee tells him that she keeps confidential documents such as corporate records, company R & D and trade reports in her computer at home, and she confesses that she is involved in back door diplomacy for Hubble, recruiting Fortune 50 types for the new Atlantic North Alliance (ANA). They talk about the ANA and Renee tells Liam that twenty-four western leaders have recently signed an accord in Brussels "to take the planet back". She feels that the new ANA alliance will be effective because resistance to the Taelons is now is a matter of national policy and not just a fifth column movement as the Resistance was. Liam feels it would be a mistake to underestimate the reaction of the Taelons to the ANA - they are very slow to change and they dislike change.

At a cocktail party hosted by the UN companion, Renee meets Hubble, who is attending the function in order to make contact with possible recruits for the ANA. Hubble and Renee chat briefly about developments at the ANA and about the break in at Renee's apartment. Hubble compliments Renee on her work for him as a power broker and mentions that she has brought Gates, Ransom and Joshua Doors into the ANA fold. He points out a blonde man across the room as Dr. Raymond Fuchs, Nobel laureate, a world player in the bio-medical field, and a man known for his anti-Taelon sentiments. Hubble also identifies a statuesque brunette across the room as Claire Yeats, chief financial officer at DonorMed, the bio-medical company headed by Fuchs. Hubble suggests that Renee make contact with Claire in order to obtain access to Fuchs, but gets a frosty reaction from Renee who tells him that she and Claire were best friends at Harvard, but that they had a falling out shortly after graduation and have not spoken since. Ignoring Renee's reluctance to talk to Claire, Hubble engineers an encounter between the two women. They reconcile (reluctantly on Renee's part) and leave the embassy together to catch up on events.

On the mother ship, Zo'or castigates Sandoval for not having dealt with the ANA threat. Sandoval is well aware of the ANA's agenda and recent developments in that regard. He is also aware that Renee is recruiting new ANA members on Hubble's behalf. Zo'or believes that the ANA and its "Earth First" attitude represent a threat to Taelon ambitions on earth. Sandoval tells Zo'or that he is collecting information and that he is keeping an eye on the situation. Zo'or says darkly that more than watching may be necessary.

Renee and Claire are sitting on the rug in Renee's apartment looking at old college photo albums. Claire tells Renee that she disappeared because she fell in love with someone named Stephen, that Stephen's parents threatened her, and that she found it difficult to connect with anyone after the affair was over. Renee is sympathetic and goes upstairs to dress for their dinner out. After she leaves the room, Claire powders her nose, then triggers a device in her compact and places it on the coffee table. She dons an optical surveillance apparatus (like that worn by the intruder), places a disk on Renee's desk and proceeds to copy the contents of Renee's computer without actually touching it.

The next morning, Liam contacts Renee. She arrives at his "digs" under St. Michael's church, wearing dark glasses, nursing a hangover and desperately in need of aspirin. Liam tells her that the intruder used her living DNA suspended in some kind of chemical tears to fool the security system and enter her apartment, and he inquires whether Renee has had any medical procedures done lately. We learn that Renee had a biopsy performed at Johns Hopkins a month earlier under general anesthetic, but that the growth turned out to be benign. Liam believes there is a connection between Renee's biopsy and the break in at her apartment, that the intruder obtained the required sample of Renee's DNA while she was a patient at Johns Hopkins. Renee is reluctant to believe that is the case, citing the impeccable reputation of Johns Hopkins in the medical community. Liam tells her that DonorMed have a clinic at Johns Hopkins for organ transplants and tissue biopsies. He finds it curious that Claire has reappeared in Renee's life at this particular time after having been absent for so long. He remarks that faking DNA is an advanced science and that nobody is better at it than Fuchs.

Renee visits DonorMed with Claire and tries to recruit Fuchs, who tells her he will consider the matter and get back to her.

On the mother ship, Sandoval meets with Fuchs who is edgy and treats him with contempt, calling him an errand boy and a bloody hatchet man for the Taelons. Through Sandoval we learn that Fuchs was once afflicted with Huntington's Corea and that he was cured by the Taelons. Fuchs tells Sandoval that he is now in possession of twenty-three pairs of chromosomes, each coded with uniquely generated DNA. He is using adaptive DNA techniques to create human specimens "from scratch" and from raw DNA material. All he needs to endow his creations with life is a single gram of Taelon core energy, but Zo'or is reluctant to provide him with the core energy and wishes to proceed cautiously. Sandoval says that Taelon core energy is tightly protected by the Synod and that Fuchs has yet to prove that he is capable of applying its quantum components to carbon-based material (humans). Fuchs is angry, agitated and anxious to continue his work, and compares himself to God because he too is able to create life.

In another location on the mother ship, Claire meets Zo'or and gives him a disk containing the information which she copied from Renee's computer. She ask that Zo'or keep his promise. Zo'or agrees and a Volunteer shows Claire into a chamber on the mother ship where her lover, Stephen is waiting.

Liam and Renee meet in Renee's office. Liam has obtained a copy of Renee's medical file which angers Renee. Liam tells her that Claire Yeats was a visitor at Johns Hopkins while her biopsy was being done, and that both Claire and Fuchs are on Zo'or's confidential visitor log; it is obvious that DonorMed is doing business with the Taelons. He asks her to replay the surveillance video made at her apartment during her evening with Claire. He points out the place on the tape where Claire used her "compact" to create a "time cut" or hologram, something to fool the security camera, allowing her to move about freely in the apartment and plunder Renee's computer. Renee confirms that the contents of her computer (and the disk which was in it) were decoded and copied without even touching the computer.

On the mother ship, Claire is talking with Stephen. We learn that Stephen, who is the exact physical duplicate of Raymond Fuchs in every way is actually a clone; Fuchs created him using his own DNA and his adaptive DNA techniques. While they are physically identical, the two men are worlds apart in their thinking and morality. Stephen feels that Dr Fuchs is dangerous and must be stopped. He discusses escape with Claire who is alarmed and urges him to remain on the mother ship.

A conversation takes place between Renee and Hubble. She reports that Claire is the intruder who broke into her apartment and copied the ANA data from her computer system. The ANA plans have been thoroughly compromised, and Hubble is furious. He wants know why Renee did not have Claire thoroughly vetted before taking her back to the apartment (ignoring the fact that Claire had already broken into the apartment at least once before she reconciled with Renee). Renee retorts that Hubble should have checked out Claire himself since he has the resources to do so. Hubble comments bitterly that they have been snookered dismisses Renee from her position as his "power broker", saying he will now have to find someone else for the job.

Liam and Renee meet at the Flat Planet Café. Liam has been researching Claire's past and tells Renee that Claire was abducted by the Taelons five years earlier and used in experiments involving synthetic brain chemistry. He has found evidence that a neural chemical bonding experiment was performed using Claire and someone named Stephen as its subjects. Renee recognizes Stephen's name from her conversations with Claire. She is upset and Liam suggests that she make contact with Claire again, using the possibility of new ANA information as bait to draw Claire in.

Stephen escapes from the mother ship after assaulting a security guard and manages to reach earth. He has never been away from the mother ship, and is disoriented by the sights and sounds of Washington. As he wanders about in the street, he is identified (incorrectly) by a security officer as Raymond Fuchs and taken to the DonorMed complex at his own request.

Renee and Claire meet in Renee's office, and Renee confronts her about breaking into her apartment and "looting" her computer. Claire tries to walk out, but is prevented from doing so by the appearance of Liam. Claire admits she was abducted by the Taelons five years earlier and held hostage on the mother ship for a prolonged period. Liam is looking for Stephen's name among the list of abducted humans. Claire tells him that Stephen was not an abductee, but a clone of Fuchs. She tells Renee that if she cooperates with the Taelons, Stephen will eventually be released and they will finally be able to live together in peace. Liam inquires about Claire having and CVI and she says it wasn't necessary. She tells Liam and Renee that the Taelons are behind everything at DonorMed including the adaptive DNA research and Fuchs' Nobel prize.

Liam, Renee and Claire learn that someone has escaped from the mother ship and that Sandoval is supervising the man hunt which is in progress. Claire realizes at once that the escapee is Stephen and she implores Liam and Renee to assist her in finding him. She tells them that Stephen is probably on his way to DonorMed to confront Fuchs. They enter the DonorMed facility and begin searching for Stephen. Liam sees Fuchs and mistakes him for Stephen. The good doctor becomes abusive and threatens to call security. Liam identifies himself as being the security Fuchs is about to contact.

At the former Resistance Headquarters under St. Michael's church, Renee tells Liam that Claire is in hiding and has registered at the Watergate Hotel under an assumed name. There is still no news of Stephen who is showing remarkable stealth and has been able to duck an entire Volunteer dragnet. Liam tells Renee that Fuchs was very tight lipid about the Taelons and would not cooperate with him in any way. He (Fuchs) is not very happy about Stephen's escape, but not overly concerned about Stephen being apprehended. Liam has discovered that Fuchs was once terminally ill with Huntington's Corea, but made a miraculous recovery and a scientific breakthrough, all within three months of being diagnosed. He believes that Fuchs may have cloned himself for insurance and as an eventual source of spare parts. He also believes that Claire's love for Stephen was artificially induced by the Taelons as part of the experiment they conducted with her and Stephen.

Sandoval and Fuchs meet in a lab at DonorMed and Fuchs shows Sandoval the perfect human specimen (with no identity or finger prints) he has created. Sandoval is impressed and says that if Fuchs is being truthful, he will return shortly with the Taelon core energy which Fuchs needs to complete his project and bring his humanoids to life. Sandoval has not been able to locate Stephen and is hoping he (Stephen) will contact Fuchs. Fuchs is angry about his work being kept secret and says he will not be kept under the thumb of the Taelons forever. Sandoval contacts Zo'or to tell him that Fuchs' ego is becoming a problem - Zo'or instructs Sandoval to prepare to eliminate Fuchs, who is becoming a liability.

At DonorMed Claire activates her portable ID portal and transports Liam and Renee into the facility. She is surprised when she realizes that their first order of business is not to look for Stephen, but to search the facility and find out what Fuchs is working on. All three are sickened when they discover a laboratory containing a number of inert humanoid specimens on life support systems who are obviously being used as a source of organs for organ transplants. It appears that Fuchs is actually running an organ farm at DonorMed. Renee asks Liam if the specimens are alive, and he says they are not.

Renee is anxious to search for Stephen, and Liam and Renee are forced to tell her that her love for Stephen may have been chemically induced by the Taelons as part of their experimentation with human sexuality. Claire tells them that the only thing missing in Fuchs project is the gram of pure Taelon core energy which he needs to spark the life force in his creations. Liam is looking at his global and says that they haven't seen everything in the lab. They locate a second chamber, this time the one in which Fuchs' perfect human specimen is lying on a gurney (where Sandoval and Fuchs met earlier). Liam examines the specimen on the table and says that it isn't a clone, but a complete humanoid with unique DNA coding except that it has no mind and has yet to draw its first breath. He refers to Fuchs work as "a pact with the devil".

Fuchs enters the laboratory and finds Liam, Renee and Claire. When confronted about his cold blooded manufacture of humanoids for organ transplant purposes, Fuchs is openly contemptuous and scoffs at the morality which allows Liam, Renee and Claire to question his work. He openly dares them to leak the details of DonorMed's activities to the media. Stephen enters the lab and tries to convince Fuchs to stop his work on adaptive DNA. Fuchs replies that (Stephen) is a host and organ replacements for longevity, nothing more. Sandoval has concealed himself in a corner of the laboratory, and seizing the opportunity to eliminate both Fuchs and Stephen at once, he fires, killing them. Fuchs is killed immediately and Stephen dies in Claire's arms. Liam searches the lab, but the shooter (Sandoval) has gotten away.

At short time later, Liam and Renee take a walk along the promenade. The ANA treaty has finally been ratified, and DonorMed has been completely shut down. Legal hearings on DonorMed's activities are in progress and Claire is the star witness in the proceedings. Renee tells Liam that Claire has had a rough time and that the hearings are difficult for her, but that "she will live". Claire appears on the scene; she is taking a brief walk during a recess in the hearings. Renee asks Liam if she can be alone with Claire. Liam leaves, and they (Renee and Claire) reconcile for the second time.