Six months after her life unraveled, Molly Woods is confined to a psychiatric hospital when she learns of a murder she worries might be connected to what she witnessed in space. Meanwhile, Julie takes charge of a newly militarized Humanichs program.
When another pregnant woman suffering from familiar symptoms emerges, Molly tries to convince her that carrying the child will kill her. Julie is exasperated by Ethan's rebellious attitude, and the military tracks the location of Molly's son.
Molly's friend Toby tries to recruit her into the operation that is tracking the alien threat, which could mean taking out her own child. The Humanichs program's fast-tracked prototype makes her morally ambiguous debut, and Ethan's reprogramming has unforeseen consequences.
Molly joins Toby's virus research team to fight the alien hybrids, only to find herself experiencing bizarre hallucinations. Elsewhere J.D. looks for help for his daughter, and Ethan decides to go out on his own in search of Molly.
Molly discovers Ethan's fate and forces the GSC to reevaluate letting Julie keep him, while Lucy reaches a landmark in her development as a weapon to be used against the hybrids. JD is convinced to help Molly investigate the suspicious death of her husband.
Uncertain of what to do after discovering that her DNA is being rewritten, Molly goes in search of her son, Adhu -- who holds the secret to the hybrids' presence on Earth. JD gets a visit from his ex-wife, and the Humanichs program reaches a new milestone.
While Charlie begins to power up the first generation of Humanichs soldiers, JD and Molly kidnap Toby to propose peaceful coexistence with the hybrids. But after the General turns on them, Molly finds it difficult to maintain her tenuous alliance. Lucy discovers a harsh reality about her programming.
In the wake of a devastating attack by the GSC the hybrids are left scattered, and Molly must trust JD's ex-wife to watch over her ailing son Adhu while she seeks out a cure. Faced with her mortality, Lucy blackmails Charlie to remove her expiration date.
Molly lies near death after she succumbs to the hybrid virus, dreaming of an other-worldly encounter with her father at a carnival. Ethan regains his missing memories so that he can say a proper goodbye, and Julie faces the reality of where her decisions have led.
Molly returns after a harrowing near-death experience to find the GSC in full evacuation, as a militant group of hybrids attack the facility -- while Lucy leads a squad of Humanichs to stop them. As Toby's allegiances are brought into question, Ethan delivers a shocking message.
Molly and JD track down John's former colleague, who reveals the true nature of their enemy and its threat to the human race. Meanwhile Charlie agrees to get closer to Lucy in order to find out where her orders are really coming from.
Molly and Ethan try to enlist Fiona's help by convincing her that the G.S.C. supercomputer is the real threat to the human race, while TAALR and Lucy prepare for their next move. Dorothy brings in an injured Tara, and JD faces the reality that he may not survive a daring mission to infiltrate the high-security G.S.C. headquarters.
With only hours before a Humanich attack threatens the extinction of the human race, Molly appeals to the hybrids for help. JD is near death after an attack by Molly's doppelganger, and Charlie and Ethan follow a lead on Julie's location.
