JD and Molly look at her newly changed triple helix DNA and discuss her bizarre alien symptoms. Molly voices her concern that she's becoming a cross-breed of species. She explains that it may have been due to the pregnancy, with the leftover alien baby cells having changed her DNA. She has JD extract her bone marrow so she can test herself.
Julie has a nightmare about the custody hearing for Ethan.
Molly remembers that she is supposed to meet up with Ethan that day and heads out. JD misses Kelsey's doctor's appointment while he's warning Molly about Tobias not being her friend. He speeds off to go meet up with Kelsey, leaving a message and apologizing for missing her appointment.
Molly goes to visit Ethan at Julie's. She tells him that he'll have to wait a bit for them to spend time together, because she's sick right now and needs to work on getting better. She tells him that Julie will take care of him until she is better.
The government discusses the evolving hybrids, with Lucy at the table. Anna mentions that the hybrids realized that the humans were tracking them via body temperature scanners and so the hybrids adjusted their core temperature, raising it to 98.6. Lucy explains that, despite the hybrids' evolution, she was able to spot the hybrid she killed by noticing he was emitting delta waves, which normal humans only emit while sleeping. The government official enthusiastically voices its intention to move forward with more Humanichs and also with generating the virus.
Molly arrives to speak with Tobias. Lucy spots her and when she scans Molly the result is "inconclusive."
Tobias tells Molly that lab coworker Nate took her virus research and ran with it, and so they'll be mass producing the effective virus immediately.
JD approaches his house, where a woman (his ex) meets him and calls him a jerk. She calls JD out on missing Kelsey's doctor's appointment. JD accuses his ex of being jealous that Kelsey came to him for help with her pregnancy first. She counters that she's angry that JD blew the second chance Kelsey gave him. She storms off, leaving behind Kelsey's key against JD's wishes.
At the Humanichs lab, Ethan plays with a remote control car that Julie got him. Lucy points out that Julie probably got it for him to appease him and make him forget his anger at her. She tells Ethan that due to her positively received actions, the Humanichs team will be making more of them. Ethan tells Lucy that Molly told him she isn't feeling well and will not see him for a while. Lucy tells him that that was probably a lie, and reiterates that all humans are liars.
Anna tells Julie that they are ordering 100 more Humanichs. Julie argues for keeping John's protocols in place. Julie remembers her confrontation with John back in the season premiere. It's revealed that after John left she immediately called Anna, who told Julie that she would "take care of it."
Molly goes to the virus lab, where she finds that she no longer has access. She confronts Nate, telling him that she needs the spores. He tells her that the spores are gone. She attempts to copy DNA sequencing onto a portable flash-drive, but she is blocked from the system. Nate calls the guards as she makes her escape. Molly calls JD and tells him she's in trouble.
JD meets up with Molly in a secluded location. They discuss that she can't control the odd alien powers she's been exhibiting. She tells him that the GSC has a virus to kill the hybrids, and that she thinks it'll kill her. JD promises she won't die on his watch.
Nate debriefs Tobias on what Molly did at the lab.
JD takes Molly to a car garage. She tells JD that what she needs to figure out if she can reverse her transformation is an exact gene pairing -- DNA from her alien son. She hypothesizes that hybrids have a psychic connection and maybe she can find him that way, by tapping into his signal.
Julie explains that Lucy's exact neural mode is being uploaded to the 100 physically ready Humanichs. Lucy asks whether they will all be her. Julie clarifies that, while their experiences will differ, their baseline algorithms will all be Lucy.
Ethan, using his toy car, finds the stash of empty Humanich bodies and other robot parts.
Tobias talks to one of his agents, trying to figure out who JD is exactly and what his possible weakness could be.
Molly and JD sit in the car, Molly waiting to get a signal from Ahdu. They try to figure out an alternative way to send a message. Molly accesses the flash drive that she stole from GSC, explaining the "help me" message that the aliens encoded.
Julie tells Ethan that she can restore his old programming at any point, but he will feel pain. He explains that he already knows his history, and Molly can't take care of him anyway (or that, more likely, she lied about not being able to care for him).
JD cleans and redresses Molly's infected marrow extract wound. While he's doing so, Molly experiences a flash of JD's memory in the Second Kuwait War he fought in. Molly and JD lie under the stars waiting for a message from Ahdu to come through. They discuss the period of time that she was in space, what it was like, and Molly's history of interest in space. They bond, discussing how the world sees them and how they see themselves. Aural fractals begin sounding; Ahdu is contacting Molly, who suddenly becomes aware of where her son is.
JD and Molly tromp through the woods, in the middle of nowhere, for hours, looking for Ahdu. They encounter a hybrid alien girl child who tells Molly they've been waiting for her. She brings JD and Molly to an entire commune of hybrids. Ahdu approaches her, welcoming Molly home.
At the Humanichs lab, Ethan makes sure that Julie is gone and reveals his tiny robot camera creation "Spyder" to Lucy. He tells Lucy that Spyder is their baby brother, and he has enough parts to make a few more, to spy on humans. He tells Lucy that she is his real family, and hugs her. Lucy encourages him to continue to build his army as she builds hers.
Molly and Ahdu discuss the situation. Ahdu calls the little alien hybrid girl his daughter. JD and the little girl (Terra) go to look at her toys, so Molly and Ahdu can speak privately. Molly requests a sample of Ahdu's DNA so she can see if she can reverse what is happening to her. Ahdu questions why she wants to stop the transformation. She tells Ahdu that Ethan needs her, and curing herself is the only way to be there for him. Ahdu accuses Molly of not understanding the larger picture; he tells her that if she is willing to learn, she will be amazed and not afraid. They link hands and Ahdu imparts knowledge to Molly. She sees a planet slowly burning up. She apologizes to Ahdu for his loss, and he states it was never their intention to harm her.
At the Humanichs lab, Julie confirms to Anna that the uploads are complete and the Humanichs are on their way to completion. Julie asks for answers about John's death, voicing her suspicions that John's death was set up. Anna shuts her down, saying she had nothing to do with the death.
Ahdu tells Molly that they didn't realize impregnating humans would kill them. He shows Molly and JD the hybrids' memorial to the humans that died birthing them. He tells Molly and JD that the hybrids have evolved, and now hybrid births no longer kill the mothers. The hybrids claim to want to coexist peacefully, and Ahdu reiterates that Molly must make her choice between the humans and the hybrids.
Molly explains the aliens' history to JD, who is convinced that Ahdu messed with Molly's mind to make her side with them. She insists that releasing the virus would be genocide, and professes the hybrid children's innocence.
Julie and Ethan leave the Humanichs lab, planning to get pizza. Otis, the elevator robot, malfunctions, bringing Julie and Ethan up to the twenty-first floor quickly and then dropping them down abruptly. Julie panics, terrified, while Ethan remains calm.
Ahdu, looking at Molly, remarks to another hybrid that he thinks they (the hybrids) have found their new leader.
Back at home, Julie sobs over Ethan's sleeping form, while Spyder spies from underneath Ethan's bed.