The mothership is damaged when a peice of dark matter colides with it.

William Boone, the Taelon Protector who secretly led the human Resistance movement three years ago, is awoken from a state of suspended animation aboard the Mothership by Sandoval. He awakens to find that the Taelons and Jaridians have merged to become a new alien species posing an even greater threat to humanity and joins Renee's crusade against the Atavus.

Renee breaks out a serial killer from prison, hoping she will be able to provide the information necessary to kill the deadly Atavus aliens, but the plan backfires.

Renee attempts to sabotage Sandoval and Howlyn's plans for producing Atavus regeneration chambers.

Renee visits Boone and shows him a crystal that can project the location of every Atavan on Earth. In an effort to retrieve the crystal, Sandoval brings Zo'or back to life as an Atavus so that she can battle her old nemesis Boone.

Renee travels back through time in pursuit of a deadly female Atavus.

Renee hooks up with Captain Michaels to investigate a pharmaceutical plant manufacturing an Atavus Hybrid vaccine. But something is a little strange about the lead scientist Dr Spangler. Ra'jel returns to lead Renee on an enlightening trip down memory lane. Why did the Taelons pick Earth? Things take a very deadly turn at the lab; Michaels is seriously injured, Dr Spangler's truth is revealed, and, as the Captain fights for his life, Renee must make an awful final choice.