As Renee begins to lose hope that humanity will survive, an old friend reappears to give her guidance and solace. Yulyn and Ra'jel will join forces to deliver the final blow to the atavus threat to mankind. Sandoval comes to term with his past, and ends the series in a very fitting "Sandoval" manner.
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.
Renee receives part of an old manuscript from an associate of her Harvard professor, who believed that ancient Egyptians were visited by aliens. He claims he has discovered proof of this and then disappears. Renee visits the Giza plateau and fins she must hook up with an old flame, in fact her love, Raleigh Sinclair, who's a dashing British scoundrel and a rogue archeologist. The two must work together to search the Pyramids to locate the tomb of Askenaton, a Grand Vizier to the Pharaohs and possible ancient Atavus who had mystical powers. Renee and Raleigh have some good hot-tempered banter as they try to outwit each other, while Sandoval arrives to complicate things further.
This pivotal episode brings Renee Palmer to a hybrid-infested hospital where comatose patients are being used as a food source for the Atavus. It is only when Renee is ultimately able to expose these atrocities that the FBI finally takes seriously the threat of the Atavus, who must feed on the life force of humans in order to survive. The FBI pledges to join Renee's crusade to destroy this formidable alien menace before they take over the world.
Renee suffers an emotional breakdown after a high-rise attempt to rescue a woman and her baby from an atavus attack goes horribly wrong. Unable to shake the image of the crying baby falling to its death, Renee and Street check into a spa to try to relax. Her therapy is soon cut short as they find themselves being stalked by Howlyn.
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.