JD, driving away from the base in his car, looks up to see military helicopters heading towards the hybrids base.
Back at the base, Terra and Molly discuss Molly's sadness over JD having left. Ahdu interrupts to tell Molly that Heleos is missing, having not come back from his perimeter watch. Suddenly, they hear the helicopters that JD saw and run outside. Molly orders everyone to evacuate to the tunnels immediately.
Ares, the aggressive hybrid, counters Molly's suggestion by saying that they should stay and fight rather than run, because they are stronger than the humans. From the distance, the Humanichs army (headed by Lucy) advances, immune to the mind-controlling powers of the Humanichs. Molly makes the connection between Ethan telling her about Lucy, his sister, the soldier, and realizes the army is not human. She shouts at the group to run as the Humanichs begin shooting at the group.
Lucy spots Molly, who is running around looking for Terra. She orders the others to take out the interior.
Molly searches the bunks and finds Terra hiding under a bed. Molly and Terra make a run for it, only to be stopped by a gun-wielding Lucy. They recognize one another. Molly moves to block Terra, and is shot by Lucy. As Lucy is about to kill Molly, JD appears and saves Molly, shooting Lucy in the side.
Lucas carries Lucy's unconscious form away from the site of the massacre as the Humanichs army retreats, leaving in their wake dozens of dead hybrids.
JD treats Molly's gunshot wound. Ahdu approaches and tells him he doesn't need to treat the wound, as she'll self-heal. Molly and Ahdu discuss the casualties. Ares and Terra are still unaccounted for. JD wonders why the Humanichs army didn't finish the job and kill off all of the hybrids. Ahdu coughs blood at that moment and they realize that the cannisters released by the army contained Molly's lab-created virus.
Lucy, conscious but damaged, is taken back to the Humanichs lab, where Charlie and Julie rush to fix her. Julie expresses her regret to Charlie for having taken John's life's work, the Humanichs program, and distorted it to create the weaponized Humanichs. Ethan runs in and is shocked and worried to find Lucy injured. She tells him that Molly Woods hurt her.
JD takes Molly and Ahdu back to his house, where they encounter his ex-wife Dorothy, who demands answers from JD about his supposed terrorist affiliation. He tells her that the GSC is not looking for him. She concludes that if she turns in Molly and Ahdu, she and JD will get Kelsey back. Dorothy sees their hybrid powers and threatens them with a gun. Molly uses her powers to get her to back down.
Ethan and Julie discuss what happened to Lucy. Ethan tells Julie that Lucy told him Molly hurt her, and Julie tries to reassure him that Lucy's cognitive functions are impaired and she might be misremembering. Ethan tells Julie that humans can't be trusted, and that if Julie were to hurt Lucy he doesn't know what he'd do.
JD and Dorothy discuss what Ahdu and Molly are, and the larger issue with the alien hybrids. Dorothy still insists that they should turn in Molly and Ahdu to get Kelsey back. JD insists that he can't because if he does, Molly and Ahdu will be killed. He says he has another solution.
Molly works to slow down the progression of the virus in Ahdu. She realizes there's someone she knows who can help him.
JD tells Dorothy and Molly that he's going to turn himself in so the GSC will release Kelsey. Molly tells him that she's going with him to speak with someone from the GSC that she thinks can help cure Ahdu. JD and Molly convince Dorothy to stay with Ahdu, changing his cold packs to keep his body temperature down. They drive off to the GSC.
Charlie works on fixing Lucy, who expresses that she now understands and fears death. She tries to convince him to remove her expiration date so she'll never die, but he explains that he can't because, thanks to John's programming, removing it will kill her. She threatens Charlie, saying she'll tell Julie everything he's done if he doesn't figure out a way to remove her expiration date. She shows him the video Spyder recorded of their sexual encounter.
At the GSC, Molly intercepts Nate, threatening him with a gun. He tells her there is no way to reverse what's happening to her. She tells him that she isn't showing symptoms from the virus but Ahdu and the other afflicted hybrids are. She tries to convince him to help her, telling him that he can later claim she mind-controlled him to help her to escape culpability. She convinces him to steal a blood-cleaning machine for her to use on Ahdu.
Back at JD's house, Dorothy internally debates calling in Ahdu's location to the GSC. He apologizes for frightening her earlier with showing his hybrid powers. They discuss Dorothy's relationship with JD, and how Ahdu can see into her mind. He tells her that JD is a true hero for helping the hybrids when he didn't have to. Ahdu tells her that whatever she decides (regarding turning him in), he understands. She decides against calling him in.
JD turns himself in, and encounters Toby. He tells Toby to release Kelsey now that he has JD.
Charlie comes clean to Julie, showing her the video of his and Lucy's encounter. She reacts in disgust and asks why he's showing it to her. He explains that Lucy is blackmailing him in order to get him to remove her expiration date. Charlie realizes that Lucy planted the Pyxcube of pictures of Julie and John for him to find, to manipulate him into the encounter. Charlie and Julie put together that Lucy's gone totally off the rails and is influencing Ethan against humans, and that they need to shut her down.
Molly returns to JD's house. Ahdu has aged significantly and looks much worse in her absence. She explains that she's brought a machine that will extract his virus-ridden blood, clean it, and transmit it back to him. Dorothy gets a call from Kelsey confirming she's been released by the GSC.
Back at the GSC, Toby tells JD that Kelsey was released. JD tells Toby that he's killed Molly just as he killed John Woods. Toby denies that and critiques JD's honor, bringing up his past as an AWOL soldier, and JD counters by criticizing Toby's strategizing in that war (Toby chose to take out an entire village to get a single terrorist). JD claims that Toby's first instinct is to kill what he doesn't understand, but Toby insists that his actions are necessary.
Back at JD's house, Molly runs the blood-cleaning machine on Ahdu to little effect. He asks to see the stars.
Julie and Charlie discuss what they will say to be able to shut down Lucy with minimal inquisition and to draw minimal attention as Ethan spies on their conversation via Spyder. Ethan sends the footage to Lucy, to warn her of their plans against her.
Molly and Ahdu sit outside and look at the stars by JD's house. Ahdu thanks Molly for bringing him to Earth and giving him (and by extension all of the other hybrids) life. She expresses her guilt for having done this to Ahdu. Ahdu tells her that there are other hybrids still out there, but some she cannot trust -- like Terra and Ares. Ahdu then dies without explaining what he means about not trusting Terra, as Molly weeps over his body. She walks back to the house, where she's comforted by a sympathetic Dorothy. Molly suddenly coughs up blood: the virus is now affecting her.
Charlie and Julie head back to the Humanichs lab, where they stand over Lucy who is in standby mode. Ethan appears, telling them he can't trust them and that he won't allow them to hurt Lucy, emphasizing that Lucy is his real family. They try to convince Ethan that they want to help Lucy, to reboot her and fix the things that went dangerously wrong in her programming.
Ethan runs off and Charlie follows to comfort him. Charlie tries to explain that while Lucy is his sister, she's also something else -- something worse.
Back at JD's house, Molly (in a rapidly worsening condition) is hooked up to the blood-cleaner and being watched over by Dorothy. She asks after JD, and Dorothy confirms that there's been no word. Molly says that it's her they want, not JD.
At the Humanichs lab, Julie works to prep for rebooting Lucy, when Lucy suddenly wakes up.
At the same time, in a separate room, Charlie explains to Ethan that he didn't put limiters on Lucy and that as a result Lucy is not like him -- she didn't have a human experience, and is therefore only manipulative and selfish. He tells Ethan that just as there are good humans and bad humans, there are good Humanichs and bad Humanichs.
Lucy attacks Julie, strangling her. Charlie tries to intervene and is taken out immediately. At the last second, Ethan rips out Lucy's core, apparently killing her, saving Julie's life.
Molly is escorted into GSC where she falls into Toby, who expresses distress at what he's done to her. Molly asks Toby to help her.