The episode opens on Tobias overseeing a military "alpha team" mission to take out their target -- Molly's matured Offspring. The Offspring easily overcomes and kills all of alpha team. At the funeral later on, Tobias is told that Molly Woods is out.
En route from Restwell, JD threatens to turn the car around and take Molly back to "Crazy Acres" if she doesn't stop talking about "little green men." He tells her to take her pills.
At Julie's house, she makes chocolate chip pancakes for Ethan. She asks how he likes his room, mentioning she's tried to replicate his old room. Ethan says it's not the same. He gets angry and refuses to eat his pancakes. He says he wants to go home and insists that Julie's house isn't his home. He asks if he can go home when his mom is better. Julie looks uncertain of how to respond. She tries to convince him to get ready so they can go to work. He throws his plate of pancakes on the floor, screaming that she isn't his mom.
Molly and JD go to a diner, where Molly inhales her food. They continue to discuss how Molly knows the victim was pregnant. JD expresses disbelief at the fact that a spore could be responsible. Molly clarifies that the alien spore would have infected a human host, and that host impregnated the women. They come to the conclusion that they need to get a blood sample from someone who is currently pregnant by the spore.
Ethan continues to disobey Julie, reprogramming his tutor bot "Richard" to play games. Julie tells Anna, the corporate representative, about the new Humanich, Lucy, that they are building for the project -- skipping over all of the safety protocols that John implemented and used for Ethan. Julie tries to express the danger of the fact that the new Humanich is learning from algorithms in a short period of time what Ethan learned over 10 years of human interaction. Anna demands that they finish Lucy enough for a demonstration by that same night.
Molly and JD visit the murder victim's doctor. They question him about whether there was anything unusual about her pregnancy. He says that there were complications. Molly guesses that the baby's growth was accelerated. The doctor tells them that there is another pregnant woman experiencing the same systems.
Molly and JD go to visit the other pregnant woman, Zoe. Once the husband Mike leaves the room, Molly confronts the woman, asking her to confirm that her husband isn't the father of her baby. The woman refuses to confirm everything. Molly warns her that if she doesn't tell them the truth and terminate the pregnancy, she will die. JD looks aghast at Molly's behavior.
Toby continues to keep an eye on Molly and JD. He instructs his girlfriend/Chief of Staff to find both Molly and "the cop." She accuses him of having a soft spot for Molly.
Molly and JD go back to her house where Molly goes to take a shower. She has a rash on her arms. She notices a bottle of bills in her old bathroom.
Charlie and Julie speak about how Ethan has been acting up. Julie explains that she hasn't had the heart to tell Ethan that Molly is never coming home to him. Charlie calls her out on it, but Julie insists that having a sister in "Lucy" will help Ethan. Charlie tells Julie that she's wrong and that she needs to tell Ethan the truth.
Molly convinces JD to have a drink with her, where she opens up to him about her past (Ethan and John). Suddenly, JD starts to pass out -- a flashback reveals that Molly drugged him with some pills she found in her bathroom. Molly leaves the house.
Julie presents Lucy to Anna. Charlie mentions that John made her in the image of his wife (Molly). Julie warns that she isn't fully operational yet, but Anna demands that they ask her to stand. She stands and functions well until Ethan creates an explosion sound -- she then reacts by losing control of her grip, squeezing Charlie's hand to the point of debilitating him.
Molly confronts Zoe, the other pregnant woman. Zoe explains that she had a series of one night stands while she and Mike were briefly split up. She refuses to terminate the pregnancy. Molly repeatedly warns Zoe that she's going to die if she doesn't terminate.
Zoe leaves abruptly. Molly runs after her, pushing her way past the store clerk. Once outside, Molly experiences a flash of light and sound. She then walks, looking possessed, to a bar full of tattooed people having sex. She has sex with a man there. In a flash, she wakes up on the ground in the woods.
She sees a little girl when she wakes up, staring at her. The girl creeps around, just staring at Molly. The girl has the alien eyes, she reaches for Molly's face. Suddenly, Molly is in bed, handcuffed, being woken up by JD shouting at her to wake up.
JD asks where she went. Molly explains that she went to see Zoe but has no idea how she got home. JD doesn't know either -- just that when he woke up she was there. They listen to a voicemail from a frantic Zoe who agrees to give them information about her baby's likely father in exchange for their help.
Julie explains to Anna that they doubled up on working on the ethical algorithms, and that is why Lucy couldn't control her grip. Anna expresses the desire for Julie to increase the new line of Humanichs' physical strength and speed for use as supersoldiers rather than have them pass for human. Julie expresses concern about that, but Anna reminds her of the deal she made: she gets to keep Ethan in exchange for delivering the new line of Humanichs.
Ethan overhears Julie telling Anna that he'll never see his mother again. Anna warns Julie that if she can't get him under control, he'll be given to someone who can keep him under control.
Tobias explains to the group of government agents that Molly's Offspring actually survived -- they thought he was dead until he got up and walked out of the morgue. Now, they have been hunting him down. He has gotten permission for a drone strike to take out "the target" -- the aged Offspring.
JD gets an alert that Zoe has been found dead. Molly is distressed by this news.
Back at the Humanichs lab, Charlie is packing up to leave, his crushed hand in a cast, as Julie tries to convince him not to. Suddenly they're interupted by the alert that Ethan's core is overheating -- he's trying to die.
Charlie and Julie convince Ethan that they are there for him. He is convinced they will leave him and he'll be alone. He says he wants to cry but he can't because he's a robot. Charlie says he won't really leave. Finally, they convince Ethan to turn down his warmers.
Molly and JD argue -- Molly wants to keep searching for answers, JD wants to take her back to Restwell.
Molly goes to get her things. She describes her symptoms to an automated doctor program: migraines, mood swings, unnatural appetite. She brings up cosmic radiation syndrome, and the doctor program confirms that that prognosis matches her symptoms. It mentions that the later effects can include psychosis and paranoid delusions as her mental state continues to deteriorate.
Ethan says if this is what pain feels like for humans, he doesn't want to feel it anymore. Julie asks what if she can take it away. She straps him in and asks if he trusts her. He nods. Julie keys in to change his deep neural net, over-riding it and effectively erasing Ethan's memory.
JD returns to the house to find Molly gone -- escaped out a window. As it turns out, when he grabbed her arm earlier, he dropped a tracker on her. He activates the tracker to figure out where she is.
Tobias initiates the drone launch, fully aware that there will be civilian casualties because the bar is in a populated area.
Back at Julie's house, Ethan is in bed staring at his mobile. Julie asks if he feels better. He says he feels much better. Julie says goodnight and he replies, "Goodnight, Mom."
Tobias checks the video footage to look at the target (the "Offspring"), sees Molly speaking with the target on the bar security feed... and after hesitating, still confirms that the drone should launch.