Five months earlier, in Santa Clara, CA, two morgue workers, talking over the Offspring's "dead" body, see it mutate. The body splits apart and a new, slightly aged Offspring emerges from it. Its eyes glow. The aged Offspring dresses and leaves the morgue, leaving his old body and the workers trembling messes on the floor. That first night, he sleeps on the street. He uses mind control to secure an apartment as a "Mrs. Nelson." He watches cartoons and listens to multiple radio pods at once and looks out the window while eating junk food and protein powder.
Over the course of five months, he ages to the young adult we caught a glimpse of in last week's episode. He watches TV (including cartoons, nature documentaries, and the news -- often all at once) in order to absorb human culture.
Skipping forward to the present day, Molly and The Offspring are at a bar as the drone approaches. Molly drinks the radioactive looking green drink that the Offspring had at his apartment. They chat, and a very drunk-seeming Molly follows the Offspring (now going by the name Adu) outside when he suggests they go somewhere quieter.
They almost kiss but Molly pulls away at the last second. At the same time, they are interrupted by a gun-toting JD who sarcastically comments that he thought they (Molly and JD) had something special. The Offspring uses mind control on JD to make him turn the gun on himself, thereby revealing himself to Molly as her alien son. She demands that he allow JD to put the gun down -- he complies. At that moment, the drone suddenly strikes.
Both JD and Molly survive the drone strike and the Offspring escapes. Molly confesses to JD that the young man was her son. They are immediately apprehended by Toby's military men.
At the Humanichs lab, Charlie and Julie work on fixing up Lucy. Ethan calls Julie 'mom' and Charlie reacts negatively to overhearing that. Julie mentions the appropriate ethics adaptors have been installed in Lucy and Charlie retorts that maybe she should install one on herself too. Julie confirms she wiped Ethan's memories of Molly, but insists she did so selflessly, only to eliminate the deep pain he was in. Anna arrives, eager and ready to see the next Lucy test.
JD is being interviewed by Shayna. She calls him out on the fake court order he used to get Molly out of Restwell. She asks what he knows of the Molly-Offspring connection. JD confirms he has a problem with authority-- she reveals he was dishonorably discharged from the military. He says he also has a problem with innocent people dying in a pointless war. JD refuses to give her any more information about what went on with Molly and the Offspring, so she sprays him with a toxin that induces three days of sleep deprivation. He says now he's too tired to talk, so she leaves him there.
Molly is interviewed as well. The interviewer asks her who JD Richter is to her and whether she was at a prearranged meeting at the bar before the drone strike. Molly says she will give him the answers he wants if the people behind the glass of the interrogation room explain to her why they blew up that bar. Toby is watching and moves to go in there, against the warning of Shayna. Molly recognizes him, and looks deeply betrayed, attacking him for ordering the drone strike.
Back at the lab, Charlie wakes up Lucy (who smiles brightly at him) under the eye of Anna. She gets up and Anna greets her. Lucy apologizes for hurting Charlie's hand, and correctly identifies Anna as a member of the group who is responsible for her development as a prototype.
Julie introduces Lucy to Ethan, who confirms he already knew her but not in her current body. They go off to play chess together. Anna and Julie discuss when Lucy will be ready for a field test. Julie insists that they need to run through her protocols first, and explains the ethical adaptor, which Charlie clarifies was designed to mimic human complexity of morality.
Anna insists that they are fighting a serious threat and need Lucy up and running as soon as possible. Charlie mouths off, insisting that the protocols are necessary for morally ambiguous situations and to reduce human casualties. Anna backs off and Julie asks whether Charlie is trying to get himself thrown off the project. Charlie says that he doesn't have to pretend he likes Anna.
Toby confirms to Molly that he didn't have her committed to Restwell, but that her brain scans were abnormal. He explains to her what happened with the Offspring and asks what she was doing at the bar. Molly insists she had no idea he was at the bar, but Toby doesn't believe her. Toby insists that he is her friend, but Molly retorts that he's her only friend who tried to blow her up in a drone strike. She demands full disclosure of information on the alien situation.
Toby explains how many women have died so far due to the accelerated pregnancies and shows her a projection of how the epidemic will increase over time. Toby explains that they have been unsuccessful in hitting the "target" (Molly's son) but that they now know she can get close and complete the job herself.
Julie reads 'The Velveteen Rabbit' to Ethan. They discuss Lucy, and Ethan mentions he likes having a sister. Ethan mentions that Lucy said she's going to be a soldier and asks whether he will too. Julie says he needs to grow up first, but that he was not built to be one.
Suddenly, Ethan glitches and sees Molly's face in place of Julie's for a moment. Julie notices and is concerned.
Shayna expresses doubt to Toby about Molly's capabilities as an assassin for the government, but she trains Molly in arms-handling. Molly is a surprisingly accurate shot.
Julie tests Lucy with morality questions. She answers the easy ones with the obvious answers, but the last, morally ambiguous question makes her laugh instead at the stated image of a pregnant woman wedged in the entrance of a cave.
Anna gives Lucy a real world example instead, of a terrorist hiding out in a school of children and whether she would blow up the school. Lucy says she would. Charlie and Julie are alarmed, but Anna is pleased with her answer. Julie insists privately to Charlie that they can fix Lucy, tweak the algorithms -- but Charlie is not hopeful about it.
Toby and JD talk while JD is still in handcuffs. Toby says he is free to go and should go quietly back to his life so Toby won't notice him. JD asks what was done with Molly Woods. Toby "strongly recommends" JD leave and forget he ever met Molly Woods.
Julie preps Lucy for her meeting with Anna's people, asking her to choose between two dresses. Julie comments that it's nice to have another female around. Lucy instead takes an overly revealing third dress out of Julie's closet. Julie questions where she got the dress and tells her to just put on one of the other two dresses because the dress she chose was not an option.
Charlie and Ethan walk through the park, drinking bubble tea, when Ethan glitches out and has a memory of being handed a balloon while out with Molly in season 1. He collapses and when he awakens he asks Charlie who Molly is.
At the lab, Lucy and Ethan play a game of chess. Lucy asks whether he likes her dress, and Ethan suggests if she doesn't like it she can print herself new clothes, like Julie does for him.
Charlie and Julie discuss what happened with Ethan at the park. He warns her that he doesn't know if he can fix the glitches from what she did to Ethan. He points out they keep making excuses for ethically ambiguous choices. Julie insists that choices for the greater good are necessary. Charlie reacts strongly against that and Julie says he can find another job if he doesn't like it. Charlie confesses that he had feelings for Julie and wanted to stay for her and Ethan, but that she isn't that same person anymore.
Toby and Molly discuss the plan to take down the Offspring. Toby clarifies that he took care of Restwell and JD, and tells Molly that calling the drone strike was the hardest thing he ever had to do. He asks whether when the time comes she'll be able to pull the trigger on her son. She says they'll find out when it happens.
Anna and Julie schmooze with the government agents who have ordered Lucy's creation. Lucy and Ethan walk in, with Lucy wearing the inappropriately revealing dress. Anna asks them to run the field test on Lucy right away, and Lucy agrees.
Lucy tells Charlie that Anna wants to run the field test and that she thinks Julie is mad at her. She flirts with him. Julie notices and is annoyed by it, and by Lucy's misbehavior in general.
Back at her house, Molly encounters JD in her living room and holds a gun on him. JD comments that Molly looks okay, though he was worried about her having gone through the same torture he did. Molly suggests that JD find another case, but JD tells her that Toby took his license. JD recounts what he experienced when the Offspring controlled his mind. He tells her he wants the full story from her.
Charlie comes over to Julie's house to put Ethan to bed. Once there, Julie asks whether he meant what he said earlier. He asks whether she thinks his quitting is for the best. She says she didn't mean it and asks him not to leave, for her. He asks why not and she kisses him passionately in response.
Molly tells JD the whole story about her experience in space and her son. He tells her he needs a drink, but when he goes for one, she starts freaking out suddenly. She tells him to get out and shoots near him. He leaves. The power starts going out, due to a surge in her neighborhood.
Molly calls Toby and tells him she realizes her son is coming for her. She expresses that she doesn't know whether she can pull the trigger because he's her son. Suddenly, the Offspring arrives. Molly, in tears, holds the gun on him. He addresses her as Mother. She questions what his mission is and he reveals he will show her -- she sees around her all of her son's Offspring and he tells her that this (he and his Offspring) are the future line. He informs her that she needs to make a choice whether she is with him/the other Offspring of the rest of the human race. Molly collapses from panic and shock.
JD drives out to a house in the woods and finds a girl he addresses as Kelsey -- his daughter. Kelsey tells him she is pregnant.
When she awakens, she sees someone entering her house and abruptly shoots, thinking it is Adu. It turns out to have been Toby, who appears to be dead.