Nate directs other workers in doing tests on Molly and looking for a cure for the virus. Fiona and Toby discuss how the virus is affecting the hybrids and how many hybrids there are worldwide. Toby goes in to visit a barely conscious Molly, apologizing to her for the poking and prodding. She tells him they should study her, to see what she might have become. He tells her he needs to get some answers from her. Molly reiterates that the hybrids are not the enemy. She accuses Toby of having stolen John's work to create the army of Humanichs. She asks him whether he killed John. He swears to her that he didn't have anything to do with John's death, but she doesn't believe he is telling the truth. Toby insists on Molly telling him how many hybrids survived and where they went.
Charlie and Julie tell Fiona about the issue with Lucy, and how she attempted to kill Julie when she overheard that they were planning on shutting her down. Fiona defends Lucy's reaction. She denies Julie's request to suspend the Humanichs program due to the fact that the army all has Lucy's programming. Charlie and Lucy decide to install the limiters in order to fix the issue.
Toby finds Julie and tells her that Molly is dying and her final wish is to see Ethan.
Nate looks at some bodies in the morgue, still searching for a cure. He opens a body bag and finds an apparently dead Terra.
Molly starts a video blog for Ethan, telling him that she hopes it can help him fill in the gaps in his memory one day. She tells him about how her own mother died when she was his age.
Molly has a dream-memory of being at the carnival with her father. He tells her that it's a special occasion, and that she's going to have the time of her life.
Toby releases JD and tells him that Molly turned herself in in exchange for JD's release. JD accuses Toby of killing Molly and demands to see her.
Back in Molly's carnival dream-memory, Molly is seeing herself as a little girl. She sees Ethan walking at the carnival with Charlie and Julie, but her dad refuses to let her confront them.
Julie and Ethan talk about him having hurt Lucy defending Julie. Ethan insists he doesn't want to hurt anyone. She assures Ethan that he has humanity and isn't like the other Humanichs. She tells Ethan that she doesn't think the other Humanichs have humanity. She tells him that Molly is very sick due to the hybrid pregnancy and explains that Molly might not get better but that what she wants most is to see Ethan. Ethan expresses happiness at that idea.
Prior to their visit to Molly, Julie takes Ethan back to the Humanichs lab and restores his memories of Molly and John with Ethan's consent.
Nate works on examining the pathology of the previous virus victims. He looks at Terra's body as they prepare to cut her open. One of the workers interrupts the autopsy to say that he's hungry.
Toby takes JD to see Molly. JD talks to her unconscious self, remarking that she turned his world upside down and that she changed him. He comments that her gift is to make the world see things, and that she's the bravest and strongest person he's met. Toby listens from outside as JD speaks to her. JD affectionately tells Molly that he needs her. Toby offers JD a bottle of scotch back in his office.
In Molly's dream, she sees Toby as a carney, juggling. Molly's dad leaves her alone to speak with an attractive neighbor woman, as Molly reluctantly goes off to play Galactic Attack, a game run by dream-hallucination Nate in carney-mode.
Back in reality, Nate and the other lab worker return to the lab to see that Terra shredded her previous skin and aged in their absence, causing a third lab worker to go catatonic. She goes yellow-eyes on them to escape.
Toby and JD drink scotch in Toby's office and discuss Molly. JD questions why they didn't engineer an antidote when they came up with the virus, and Toby counters that they were strapped for time. JD explains that terrorists aren't born but made, and again brings up Toby's questionable practices when at war. Toby reiterates his philosophy of going with the lesser of two evils, while JD says that evil is evil regardless. Toby brings up that Molly believes Toby killed John. JD also says that he believes that. Toby protests again, but admits he believes that John was killed.
Julie goes in to see Molly before Ethan. She talks to unconscious Molly, explaining that she brought Ethan to see her. Julie explains that, months back, they were going to shut Ethan down permanently, so she took Ethan in order to save him. She also explains that she altered his memories to save him from hurting so badly. She mentions that John loved Molly to the very end. She admits that she thinks she may have somehow gotten John killed, and promises Molly that she won't make any more mistakes.
In her dream, Molly switches back and forth between her younger and older selves as she looks for her father at the carnival. She remembers seeing her father having sex with the neighbor woman and realizes that her father brought her to the carnival as a cover for his tryst.
Vowing that she won't make another mistake, Julie tells Charlie to shut the Humanichs program down. Charlie warns her that they could go to jail for that but heartily agrees to move forward with it.
Terra hypnotizes a guard to get him to open the security doors. The doors open and she lets in Ares and the other Hybrids. He remarks that they tried Ahdu's way (peacekeeping) and are now trying it his way. Ares makes the hypnotized guard kill himself.
JD and Toby discuss the suspicious circumstances of John's death and JD explains the timeline of Julie making the call to the restricted number. JD says he now believes Toby had nothing to do with it. Toby says there are people above him who always get what they want -- whatever the costs. JD asks whether John had any enemies. Toby tells him that he had one enemy outside the GSC, Nicholas Calderon. JD notices the security camera in the room and tells Toby that the hybrids have breached security.
Charlie instructs the Humanichs crew to assist with physically disassembling the Humanichs, since the Humanichs had adapted to resist being shut down. Just as they begin, there is an announcement for all Humanichs to be deployed to the GSC for the hybrid security breach issue.
In her dream, Molly goes to a tent and watches video of her memories of her life with John and Ethan. Her father tracks her down and tries to convince her that she misunderstood what she saw between him and the neighbor woman. In the background, footage of Molly's memory of confronting John about his infidelity plays. Molly's father's phone rings and she recounts how he answers and is told that Molly's mother died in a car crash while he was having his affair at the carnival.
Molly runs away from her father towards a sign pointing towards her final departure but on the way finds Ethan, who tells her that he is lost. She says that she's lost too. She points out Julie but Ethan counters that he wants his real mom. JD appears at the carnival and asks her if she's alright. She tells him she isn't. Molly hears Ethan's voice begging her not to go and telling her that he's there with her.
Toby calls Charlie and tells him that if he doesn't deploy the Humanichs, the hybrids will kill everyone at the GSC. Charlie points out that Ethan and Julie are there. Charlie makes the decision to take the Humanichs off standby mode and deploy them to the GSC, against his better judgment.
Molly wanders around her dream-memory carnival, approaching the final departure line. Back in the real world, Molly starts to go into a critical state as a guard warns Ethan and Julie that the hybrids are approaching.
In the carnival dream, Molly's father tells her that she doesn't need to take that ride (to death) right now. JD approaches and asks what's going on. She asks JD and her father, as projections of her own mind, why she shouldn't get on that ride. Her father encourages her not to give up, though she has every right to. He tells her that mistakes make people human, but that forgiveness gives people humanity. He tells her it's time to forgive him, John and herself. She expresses that she should have been a better wife and mother. Her father tells her that with her the human race evolves. Molly hesitates before getting on the ride. She goes through the turnstile but Ethan gets her to stop and want to go back. The ride operator tells her it's too late and that she's made her choice. Molly steps into the light as she flatlines in the real world. The guard pulls Julie and Ethan away, leaving Molly to die.
Ares and Terra go to a secure viral containment to release viruses to kill the humans.