Augur has given Liam an apartment of his own over the Flat Planet Cafe and is showing him around the place. They pause in front of a piece of modern art hanging on the wall and Augur tells Liam that it may not be much but he has spent many an hour "kicking back and enjoying the sights". When Liam gives him a puzzled look, Augur shows him that the art on the wall is actually a hidden monitor which allows the apartment's occupant watch activities in the café below. Lili and a female acquaintance are in the café talking and laughing, and Augur bets Liam that they are talking about sex because "nothing else gets that kind of a laugh". Liam is puzzled and asks Augur why. Augur tries to explain sex to him, but gets flustered and gives up. He tells Liam that sex is something he will have to figure out for himself.

Augur and Liam leave the apartment and enter the Flat Planet Cafe where they meet Lili and her friend having a drink and still talking. Liam, who has limited experience with other human beings, particularly the female gender, is fascinated by Lili's friend. Augur tells Liam that he has a wager with Liam that they were talking about men, and Liam corrects him, saying: "No, you said they were talking about sex." Augur is rather flustered by Liam's comment.

Lili denies that they were talking about men or sex, and tells Augur about Da'an having shared himself with her (The Wrath of Achilles). She says that Da'an shared everything with her, that for a moment she even joined the Commonality, and that it was the most unbelievable experience of her life, "on every level." Without being specific she lets Augur think that the experience was sexual, but when Augur leaves, she tells her companion that the experience had nothing to do with sex.

The curious (and provoked) Augur returns home, and tells his computer to identify the harmonic frequency which is Da'an's unique signature within the Commonality. She (Holo Lili dressed up like harem girl) isolates the frequency for Augur. At his instruction Holo Lili reproduces the frequency, allowing Augur to tap into the Commonality and severing Da'an's link with the Commonality.

Zo'or, now leader of the Synod, and Da'an are discussing Jonathan Doors when Da'an's link to the Commonality is severed and he suddenly reverts to an Atavus (a Latin word meaning distant, primitive ancestor). Zo'or summons Sandoval and tells him that something has befallen Da'an and Sandoval orders Lili to locate Da'an. Lili is en route to Da'an's office when she encounters the Atavus, who says to her, "You of all people cannot see me like this." The Atavus flees from the scene and Lili, unaware that she has just seen Da'an, goes on to his office to look for him.

Sandoval contacts Siobhan Beckett in London and asks her to come to Washington to assist in the search for Da'an/the Atavus.

Zo'or has called a meeting with Sandoval, Lili, Liam and Siobhan. Liam and Siobhan find themselves together on the way to the meeting and Liam tries to strike up a conversation with his mother. Lili pulls him aside and reprimands him, telling him that he must stop; if Siobhan remembers and recognizes him as her son, her CVI will self-destruct and kill her. Liam is crushed, but he obeys her. Zo'or tells them that Da'an no longer exists, having become an Atavus, and that he must be apprehended and killed. A Taelon cannot return to its original form and to the Commonality once its link is severed. He warns those present that the Atavus possesses unnatural strength, cunning and reflexes, that it possesses a functioning Sha'karava, and that it has the power to drain the life force out of anyone it encounters rather like the mythological vampire. A buried memory from Liam's alien heritage surfaces and he realizes that Zo'or is discussing (in veiled terms) the ability of the Atavus "to reshape the flesh," or to shapeshift. It was the ability to reshape the flesh which allowed the ancestors of the Taelon race to evolve into Taelons after the Commonality was formed. Since only a skrill is effective against the Atavus, the group split up, Sandoval and Lili in one shuttle, Siobhan and Liam (who does not have a skrill) in another shuttle.

The Atavus leaves the embassy and kills the first person it meets, draining the life force from him and leaving only a shrivelled husk behind.

In the shuttle, Lili and Sandoval discuss the situation. Lili wants to help Da'an and Sandoval tells her that if there were even a small part of Da'an remaining, his CVI would compel him to help Da'an, but that he senses nothing whatsoever of Da'an in the Atavus. Lili still wants to try. At that moment the news of the first murder is relayed to them, and Lili says that Sandoval may be right, since Da'an was incapable of killing.

Liam is piloting the second shuttle and Siobhan is trying to learn more about him, saying that his file mentions numerous medals and commendations, but nothing of his family background. She says that he might have sprung fully formed from the earth to judge by his file. Liam desperately wants to make contact with his mother, but cannot do so, knowing that it would kill her. He tells Siobhan that he was the abandoned child of a mixed marriage. With tears in her eyes, Siobhan asks Liam what he would say to his mother if he could talk to her now and he says, "I love you." He tells Siobhan that although he was abandoned at birth, it makes no sense, that there is a bond between him and his mother which cuts across all boundaries. His face is a study in pain and loneliness.

The Atavus kills again and Liam plots its path, based on its movements. He realizes that the Atavus is moving directly toward Augur's abode and contacts Lili. Lili warns Augur before she informs Sandoval, telling him only that the Atavus is headed for a warehouse and that it can be apprehended there. On route, Sandoval remarks that Lili called the Atavus "it" and suggests that she is beginning to realize that Da'an is beyond help.

The Atavus arrives at the warehouse and trashes Augur's computer systems just as Augur is leaving. Although Lili and Sandoval meet the Atavus face to face, it manages to get away from them and when Sandoval pursues it, he is seriously wounded. A moment later Siobhan and Liam arrive and an ambulance is summoned. Liam tells Siobhan to accompany Sandoval in the ambulance; he will contact her when the Atavus has been located.

Liam and Lili have the brilliant idea of recreating Da'an's harmonic signature in order to lure the Atavus to them. Augur agrees that it can be done, but says that his systems have been destroyed and that there is only one other computer system which is capable of doing the job, the one at Resistance Headquarters He tells Lili and Liam that even "ET couldn't phone home with this!"

When he is told of the plan, Doors, says, "Over my dead body!"and Liam replies "If that's the way it has to be." Doors is forced to back off, but he tells Liam, that it isn't over between them. As Augur logs on to the system, Lili gets her first look at Holo Lili and is furious to discover that Augur has programmed a docile subservient and very alluring version of her into his computer.

Liam enters the hospital, going directly to Sandoval's room where he finds Siobhan sleeping and awakens her. Siobhan has placed her Sowelo rune pendant in Sandoval's hand as protection, and Liam's conversation with her centres on her devotion to the runes and her use of them to guide her in her work. She tells Liam that he looks as though he has a puzzle in him and gives him a rune to assist him in solving it. Liam correctly identifies it as Raido, the rune of communication, and Siobhan is surprised that he knows the runes. (Since Liam has full knowledge of his parents, his knowledge of the runes comes from Siobhan herself, his mother.)

Liam is still at the hospital with Siobhan when Lili contacts him and tells him the Atavus has responded to Augur's signal and is at the church. As Liam and Beckett are leaving, Sandoval awakens briefly and says, "Of course, you two are together." Beckett is taken aback by the remark and asks Liam what Sandoval meant, but he doesn't answer her and they leave hurriedly for the church.

At the church Lili confronts the Atavus face to face and tries to reason with it. The Atavus seems to be responding to her reasoning when Siobhan Beckett enters. Lili tries to stop Siobhan from firing at the Atavus, but Siobhan throws her aside and fires, using her skrill. The Atavus fires back using its Sha'karava and Siobhan is thrown unconscious against a wall.

Liam stares directly at the Atavus, holding out his hands. He activates Sha'karava and begins to walk toward the Atavus. The Atavus stares back at Liam, holding out its hands, and energy begins to flow between the two sets of Sha'karava as Liam begins to reverse Da'an's transformation into an Atavus. Before Lili's eyes, the Atavus changes shape and becomes Da'an once again. Da'an is sickened by the murders he committed in the Atavus state and Lili tries to reassure him, saying that it wasn't him. Da'an tells her that everyone has a dark side, even the Taelons, and that he will never be whole again.

Beckett is taken to the hospital after her skirmish with the Atavus and Sandoval who is still in the hospital himself goes to her room to visit her in his wheel chair. Siobhan asks him what he meant earlier. Sandoval gives her a thoughtful look and says he doesn't remember, that he must have been delirious. Siobhan asks him if Lili was disciplined for insubordination for trying to stop her from killing Da'an. Sandoval says, no, she was not disciplined, because she was right and Da'an recovered.

In the final scene Doors and Lili are in the Resistance Headquarters debating Liam's actions. Doors says that Liam can't be trusted, and that he will never again set foot in headquarters. Augur who is looking at the surveillance monitor says that Doors can tell Liam himself, as he is on his way down in the elevator. As Doors walks over the elevator, the doors open and he sees Liam standing in the entrance. Liam steps to one side, revealing Da'an who is standing behind him in the elevator. There is a stir in headquarters and everyone present stands up. Da'an extends his hand to Doors in friendship and peace; Doors takes Da'an's hand for a moment, but suddenly pulls away before Da'an can begin to share himself . Everyone in the headquarters applauds.