Molly is in the empty carnival, holding a pendant. JD staggers up, bleeding, and asks what she did to him. Molly looks down at her hand and sees that she is holding a gun. She drops the gun and closes her eyes, as she flatlines back in the real world. On the hospital bed, she suddenly revives, looking old, wizened and gray.
Ethan tells Julie that they shouldn't have left Molly, though Julie tells him that she was dead and there isn't anything they can do. He breaks away from Julie and runs back toward Molly's room.
Trapped in an elevator when the hybrid security breach lockdown hits, JD and Toby get out by triggering the elevator's fire alarm. JD refuses to leave Molly, dead or alive, and leaves Toby to go find her. Meanwhile Molly, not dead but aged (the way Ahdu looked shortly before he died), coughs and regains consciousness.
Julie, running around looking for Ethan, sees Lucy and the other Humanichs on the security camera scoping out the building. She wonders how it is possible that Lucy is "alive." The Humanichs enter the room and Julie hides from them.
In the hospital room, Molly begins to molt, revealing a fresh new skin and hair beneath.
A fully revived Molly bangs on the glass walls of her hospital room, screaming for help. Her eyes go yellow and she sees Terra setting up the explosives. Ethan comes back and sees her alive, opening the door for her. They embrace and he tells her he knew she'd come back. She asks "Back from where?" and he tells her she died. JD finds Molly and Ethan, and says he thought they lost her. He warns Molly that Ares is looking to blow the place up and they need to leave. As they leave, JD notices the dead peeled away skin.
Nate sees the three of them and fills them in on what's going on (hybrids in the virus containment area, hostage situation) and also expresses disbelief that Molly is alive. Nate warns Molly that the Humanichs have been instructed to shoot hybrids on sight. As Molly's eyes go yellow, she has a vision of Terra setting up the bombs to release the contained viruses. Nate tells Molly she has to get out of here and then runs away. Molly bangs on the door of the containment unit, shouting to Terra to let her in. Terra opens the door for Molly.
Molly sees that Terra is holding Toby hostage, under her hybrid "thrall." Under Terra's hybrid influence, Toby tells Molly that he's always loved her.
Nate encounters the Humanichs, locking down the elevator to the virus containment area. Lucy demands that he allow them entry. When Nate refuses, citing that they need Toby's express permission. She says that she will use violence if he doesn't comply, but Nate claims that to do violence against humans is against robot protocol. Lucy snaps his neck and says that she isn't a robot.
Molly tries to talk Terra down from setting off the bomb, saying she will set off a war by creating the explosion. She tries to convince Terra that this is Ares' plan, not hers. Molly tells her that Ares left her there to die. Terra releases Toby from her control. Terra claims that Molly is not one of them. Molly tells her that after the events of the day, she has fully shed the last of her old life after the events of the day and has awoken with clear eyes. Terra expresses doubt that she can escape alive. Toby tries to convince her that she doesn't have to die, but she accuses him of being a murderer and wanting them all dead. Toby denies it, saying she's too young to die. Toby tells her that he can get her out of the facility safely. Molly removes the detonation device from Terra's hand and deactivates it.
JD and Ethan enter the containment area and JD tells them they must leave immediately. Everyone (except Toby) heads out. Toby gives JD a gun and requests JD's handcuffs. Ethan has a flash of what Lucy did to Nate. Terra realizes he is a Humanich. Molly clarifies that not all Humanichs (like hybrids and humans) are killers.
Lucy and the Humanichs enter the containment area and encounter Toby, who tries to misdirect her and the Humanichs to the South Wing and away from the escaping Molly, JD, Ethan and Terra, who are in the evac tunnels. Lucy tells the other Humanichs to check the evac tunnels, telling Toby that a higher power instructed her to do so.
The four escape as a smaller explosion is set off in another area of the building, away from where Toby is. They make it to a bunker JD knew about, where they watch a TV news update citing them as terrorists and blaming the explosion on them. JD guesses that Ares left the explosion as a "parting gift." Molly agrees that someone is setting them up. JD suggests it was Toby, but Molly denies that possibilty. Terra tries to leave the bunker, but Molly stops her, saying she'll figure the whole thing out and embracing Terra.
Toby is debriefed on who died in the explosion. Fiona tells him that very few people have the security clearance to know about the evac tunnels that the hybrids escaped by. Toby tells Fiona that they believe Molly flatlined prior to the explosion, but she wants to see Molly's body, substantive proof that she is actually dead. Fiona also requests a list of everyone who has security clearance and knew about the tunnels, telling him they may have a mole.
Fiona questions Lucy about the particularities of Nate's death. Lucy confesses that she killed him and had to take swift action, breaking his neck him because he was keeping them from the virus containment, protecting someone (though she tells Fiona she does not know who). Fiona says it was regrettable, but necessary. Lucy agrees. A government agent reports that all bodies were accounted for except for Molly Woods. Fiona commands Lucy to dispatch a team and bring Molly in -- dead or alive.
Julie barges into Toby's office, telling him she lost Ethan. Toby reassures her that Ethan was not among the casualties. Julie tells him that if Lucy finds Ethan, she'll hurt him and explains that Lucy attacked her and Ethan protected her by pulling her circuits out. Toby expresses shock that a Humanich attacked a human. She tells Toby that Lucy was decommissioned and that somebody went above her to put her back in action. Julie mentions her theory that Anna is the only one who could have reassembled Lucy following her disassembly by Ethan, and that she suspects Anna had something to do with John's death. Julie tells Toby that she thinks Anna put Lucy back together because she can't think of who else it could be. Julie leaves and Toby looks up the latest file on Nicholas Calderon.
With Terra and Ethan asleep, JD and Molly discuss how her skin had molted back in the hospital room. She tells him that she's changing and that she was given a second chance at life, saying she is now stronger, more alive, and about her visions. JD asks about what she saw. Molly remembers having a disturbing vision in the carnival dream, seeing JD bleeding out and her holding a gun as he asks what he did to her. Before she can tell him about it, she gets a message from Toby asking her to meet.
Molly tries to leave to go meet Toby, while JD tries to stop her, citing that her image is everywhere and she'll be spotted. He offers to have his friend make them all disappear, allowing them to escape to somewhere safe. Molly reiterates that there is no safety and that she needs to see them through the current situation -- that they won't be safe until she does. JD tells Molly that the universe brought them together. Molly reiterates to him that they need to finish what they started. As Molly leaves, JD gives her a hood to block facial recognition from security cameras and gives her a gun to use against the Humanichs. He kisses her before she leaves and tells her that he'll see her soon.
Lucy confronts Julie in a parking garage, telling her she needs to find Molly Woods. Julie tells her that Molly died, though Lucy doesn't quite believe her. Julie warns Lucy that there are cameras everywhere, and Lucy retorts that she shouldn't have tried to kill her. Julie questions how she could be alive, and Lucy tells her that that information is classified. Lucy warns Julie that if she finds out Julie lied to her, she'll be very angry. She also tells Julie to say hello to Ethan for her.
Molly meets up with Toby, who tells her that a Humanich killed Nate. Molly expresses disbelief and Toby tells her about Nicholas Calderon, John's partner in the Humanichs prototype who went off the rails after they had a huge falling out. They consider that the Humanichs are now answering to Calderon and that Calderon may have killed John when he found out John was going to confront him about hijacking the Humanichs project. Toby tells Molly that Calderon may have an ally in Taylor, the AI machine that Toby uses for threat analytics (that was created by John and Calderon), and that therefore all of Taylor's sensitive data may now be in Calderon's hands (including all the information about the hybrids). Toby tells Molly he'll find and take down Calderon but that she and the others need to disappear.
Back at JD's bunker, Ethan wakes JD up, saying he can't sleep. Ethan tells JD that normally he plays a game, like spherical chess, when he can't sleep. JD offers to teach him something else rather than chess. JD teaches Ethan how to play Texas Hold 'Em and Ethan picks up the game immediately. Ethan asks what JD's intentions are with his mom. JD tells Ethan that his intentions are to keep all of them safe. Ethan starts glitching and then abruptly shuts down to run a diagnostic.
Molly gets back to the bunker, where JD tells her that there's something wrong with Ethan. Ethan reboots and tells Molly he's overloaded. She does a hard shutdown on Ethan. She says they need to get him help right away or he might have permanent damage. JD and Molly leave to get Ethan help, telling Terra to lock the door behind them. JD tells her that they'll leave first thing in the morning.
Lucy tells Fiona that she hasn't found Molly yet. Lucy shows Fiona the footage of Toby handing JD the gun, and tells Fiona that they have a traitor in their midst.
Molly and JD bring Ethan to Julie for repairs. Julie works on him, noting that it seems his processors are working on something else. She tells Molly to make herself a drink and that she has it handled
Toby talks to Taylor the computer about Calderon, questioning him about Calderon's whereabouts and asks when the last time was that Calderon accessed him. Taylor tells Toby that he cannot say, due to Toby's clearance being revoked and the charges brought against him. Toby is captured by Fiona and her men, with Fiona citing his crime of treason in aiding an enemy.
Molly tells JD about the Calderon theory and that Toby is taking care of Calderon. JD expresses doubt but says that their papers for disappearing are waiting for them when they need it. JD questions Molly about her carnival dream-vision. Molly again flashes back to her vision of a shot/dying JD. She tells him what she saw, and that she thinks she killed him. JD laughs it off, saying she's not the first woman to have that dream and reassures her that it was just a dream.
Julie interrupts, calling Molly in to see Ethan. Julie expresses that she doesn't know what's going on. Ethan suddenly reboots and says that he has a message for them from his father.
Toby tries to explain the situation to Fiona, telling her that the Humanichs have been taken over and are being commanded by Calderon. Fiona tells Toby that Shayna sent her a note warning her of Toby's obsession with Molly and that he's been compromised. Toby tells her that they've all been compromised , and that they are on the wrong side of the war. He claims that Calderon amped up the hybrid threat (using intel from Taylor) to build up an army of Humanichs at his command. Fiona dismisses him, saying he needs a lawyer and a psychiatrist.
Terra watches the news as someone knocks at the bunker door. She opens the door to Ares, who greets her and tells her it's time to come home.
Toby tries to convince the soldier leading him to captivity to unlock his handcuffs. He knocks out the guard and escapes in a car.
Ethan speaks in John's voice, relating his message. John's message is that if she's hearing the message, it means he's dead. He says that if this message is sounding it is because a Humanich has killed a human, and that she needs to find a talisman on a chain entrusted to Calderon, as he is their only hope. Molly recalls holding that very same trinket in her hand in her carnival dream-vision. JD asks Molly whether Calderon is their savior or the devil. Molly says maybe he is both.
Toby is pursued by an aircraft as he drives away, and he tries to call Molly. As he connects with her, the aircraft releases an explosive at him.