Six months after her life unraveled and dark secrets were revealed, Molly is confined to a psychiatric hospital when she learns of bizarre deaths that sound eerily similar to those she witnessed in space. When she escapes to investigate, she crosses paths with JD Richter, a determined cop who just signed on to the case. Jeffrey Dean Morgan joins the cast as JD Richter.
The second hour of a two-hour episode, Molly tries to reconcile whether she wants to be loyal to the aliens or remain loyal to the humans. JD becomes skeptical of the aliens after one gives him a flashback to his days in combat.
After a Global Security Commission raid on the hybrid compound, Molly desperately tries to save her son Adhu, while JD attempts to rescue his daughter who is being held captive by Shepherd. Meanwhile, Lucy becomes more of a threat to humans.
Molly and JD frantically race to the hybrids to stop a Humanich plot that will destroy the human race. Also, Lucy has a shocking realization about the GSC that forces her to question her allegiance and put Ethan at risk.