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.

After he sets up an Atavus fan Web site, a disaffected teenager is used by the Atavus to recruit the world's youth into its army of hybrids.

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.

The joining of the Taelons and the Jaridians create the Avatus race, a greater threat that Renee leads the fight against.

Sandoval strikes a deal with the Atavus while Renee tries to convince Hubble Urick about the existence the aliens.

Renee, with a former reporter, tries to inform the media about the Atavus.

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.

Renee is put on trial for opening an Atavus stasis chamber.

Renee fights to destroy the Atavus as they begin a joining process that will create human-Atavan hybrids.

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

Renee has a change of heart and sympathy for her unwilling enemy as she becomes aware of the inhumane treatment the atavus hybrids must endure in government run internment camps.

Renee's personal image of mankind's greatest enemy is forever changed when she becomes emotionally involved with a young atavus child, Yulyn, whom reveals he has a very human-like soul. Renee must now protect Yulyn, also a royal, from Howlyn's evil clutches.

J Street has become an Atavus hybrid, Renee rushes to locate an antidote.

Renee and boyfriend Captain Michaels "do-the-right-thing" as they risk their own personal integrity in an attempt to secure plans to the one military weapon that can kill the atavus.

Liam and Renee investigate a serial killer who murders people in their dreams.

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.

At a Conference of Psychic Sciences, "The Commonality" the Taelon psychic link has been invaded and the secret plans for Earth are known. Katya Petrenko possesses incredible psychic gifts and an interest in Boone. She confronts Zu'or, telling him that the Taelons must change their approach to humans, or they will destroy both races. Katya reveals that a taelon named Ma'el gave some humans the gift to break into "The Commonality". As Katya dies, Dr. Belman performs a brain transfer of all of Katya's knowledge to Boone.

Liam and Augur are thrown into a parallel dimension when their shuttle flight is sabotaged by Doors. Maiya captures them and brings them back to her Imerian Resistance camp, where they start to find counterparts of people they know. The counterpart Taelons capture the colony and takes them to the mothership.

When Zo'or contracts an ancient deadly plague for which there is no known cure, Renee suggests to Liam that the virus could be used to create a biological weapon to fight the Taelons. She recruits Augur to research the virus and it's potential.

Boone is caught in the middle of his double life when his old flame comes back in his life claiming to be working against the companions.

Ne'eg dies from being exposed to a devastating virus that was unleashed from an alien probe. The virus falls into the hands of a group of white supremacists, they release the virus into the Lincoln Hills homeless shelter. The deadly virus quickly spreads, threatening to decimate both the human and Taelon races. Boone, infected with the virus, comes up with an idea to develop anti-bodies against the virus but it may not be in time to prevent the virus spreading over earth.

Working on the New York to Bangkok inter-dimensional link, a technician is killed by energy-eating creatures. Liam and Augur suspect the creatures may be from another dimension, and will drain every energy source on earth. The mothership becomes infested with the creatures, leading the Taelons to put themselves into a near-death state to protect themselves.

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.