A construction blast unearths a grave marker belonging to a Taelon scout sent to size up earth for Companion occupation thousands of years ago. Boone must find the grave which contains the research, before Sandoval finds the grave. Da'an loses his position as the United Nations Companion to Zu'or, but keeps the American Companionship.

A holographic image of Rayna, who was consumed by an alien probe, tells Augur that the Taelons are dismantling the probe which will kill her, and they will learn about the Resistance's secrets. Hearing of Rayna's appearance, Sahjit is determined to bring her back. The Taelon lab is under intense security and Augur hires a special operative, Michael Sloane, to lead the resistance team to infiltrate the Taelon compound to destroy the alien probe.

Nine hours after Beckett conceived, her child is born. The Resistance must decide what to do with Beckett and her rapidly developing child, Liam Kincaid, who reaches maturity within hours of being born. Sandoval reveals Boone's ultimate fate to Lili. Rayna transmits a signal to the Jaridians, an alien race. A Jaridian probe replicant assassin is sent to destroy all Companions. At Boone's funeral the Taelon Synod leader, Quo'on, is assassinated, but Liam saves Da'an. Da'an appoints Liam as his personal protector. Zo'or realizes that if the replicant kills Da'an, then he'll be made synod leader by default.

Augur taps into the Taelon Commonality, breaking Da'an's contact with the Commonality. Da'an regresses into the "Atavus", a pre-historic version of the Taelons. Zo'or tells Sandoval to kill Da'an. Da'an is a threat for the Atavus only has a hunger for life spirit. The Resistance lures the Atavus to try to save Da'an.

Beckett's CVI begins to break down, causing her to slip and fall while climbing in a cave. Unconscious, she hallucinates a trial for her crimes against humanity and for collaborating with the Taelons. Liam and Augur try to find Becket before Sandoval finds and kills her.