Liam, the Taelons, and the Jaridians have disappeared but their efforts, far from saving everyone, have doomed the galaxy: they have awakened the Atavus, a race of energy vampires that preceded the Taelons and Jaridians. Renee and Street are the only ones who know the truth of what's happening: the Resistance is disbanded and the human governments are in no rush to accept the beginning of another war with an alien race. Their only ally is Raj'el, the first and now the last of the Taelons, who is forced to provide covert support from the heart of the Taelon mothership.
To make matters worse, Sandoval, left in control of the Taelon mothership, allies with the Atavus leaders Howlyn and Juda. Together, they are able to keep their presence hidden for much of the season. Their plan is to create an army of Atavus-Human hybrids by means of a joining process, then use the hybrids to awaken other Atavus hives hidden around the world.
As the season progresses, a few familiar faces re-enter the fight: William Boone is brought back as a trap for Renee, but he quickly joins her side. In response, Sandoval and Howlyn revive Zo'or, giving him a new body as a female Atavus, but Renee and Boone are able to defeat their nemesis once and for all.
Final Conflict comes to a head when Liam returns to help Renee stop Howlyn from unleashing his elite warriors from the long-buried Atavus mothership. At the end of the series, Liam, Renee and Raj'el depart in the Taelon mothership, resolving to bring the few trustworthy Atavus home and indulge in a little adventure along the way.