JD, bleeding out on the floor, hallucinates being at an OB-GYN appointment with his daughter Kelsey, where the fetus' eyes glow like a hybrid and Molly in a doctor's coat tells him they've had to terminate and shoots him point blank.
Terra takes Molly to the hybrid camp led by Ares. Ares rejects them, accusing Molly of being "the hand of death" for having engineered the virus that killed so many of his people. Molly explains to the hybrid group that a virus will be released, killing humans and hybrids alike, and that their enemy is not human.
Lucy reports to Taylor that the Humanichs carrying the virus by plane will land with the virus in two hours and twenty minutes. Taylor tells her that they will now enact the final plan: to eliminate all life forms threatening their existence. He tells her that she must follow Molly-X's (the Molly Humanich replica's) orders, while Lucy visibly bristles at the idea of not being in charge.
Charlie and Ethan search for Julie in the lab. Julie, meanwhile, is fifty feet below sea level in a box, with 1% oxygen remaining. They tear the storage room apart until they find her and carry her out, avoiding the security drones.
Molly returns to the house and finds JD near death. She uses medical equipment in the house to give JD shots of her blood.
JD, still out of it and partially delirious, sees Molly and, thinking she's a threat, grabs his gun to shoot her. Molly tries to convince JD that it wasn't her who shot him. She gets into his head via her hybrid powers to see what really happened. She sees JD's memory of a duplicate of herself shooting JD. Julie, Charlie and Ethan arrive back at the house.
One of the Humanichs on the plane carrying the virus smiles at a young girl and turns over the virus in his hand.
Molly X, Lucy and the other Humanichs break into the apartment, where they are greeted only by Richard who tells them that the group left 15 minutes ago. Lucy shoots Richard. The video feed from Richard is transmitted to Molly, Julie, Ethan and Charlie, who see that there is a Humanich duplicate of Molly running around.
Molly explains to JD that the GSC created a Molly Humanich. JD sees that he is fully healed, and he realizes that it's because Molly gave him her blood. He is upset at the idea of turning into a hybrid, telling Molly that it wasn't her choice to make.
Charlie and Julie interrupt Molly and JD to tell Molly that if they succeed with shutting down Taylor, it will most likely kill Ethan as well since he is a Humanich. JD goes outside to comfort Molly, who is distraught at the idea of sacrificing her child to take down Taylor. She expresses that she can't and won't make that decision. Ethan shows up, and tells Molly that he is prepared to make the choice, to make the sacrifice for the greater good. Molly tells Ethan that Julie and Charlie are working on a way to protect him. Ethan counters that if it doesn't work, they both know what needs to be done.
Charlie and Julie work on an antivirus for Ethan, which would counteract the amulet virus that they plan to upload into Taylor's network.
The group discusses the plan to get into One Euclid to reach Taylor's server. JD expresses doubt that they can trust Ares. Molly states that the first step is to destroy the dozens of Humanichs guarding One Euclid. They turn Ethan's Spyderbots into bombs to accomplish this.
Julie starts connecting to Ethan's neural net to upload the antivirus program devised by her and Charlie.
Ares and the other hybrids show up and use their powers to shut down the power in the building.
JD, Molly and Charlie take out several of the Humanich guards and manually open the door to Taylor's server.
Julie sees that she has been blocked from accessing Ethan's neural net and is unable to complete the antivirus upload to protect him. They hear gunfire outside the door and huddle together.
Molly taps into the hybrid connection to see that the hybrids have all been taken out. Ares psychically warns her that "they" are coming. Molly is confused to see that the maze to the server that she memorized has changed. Doors shut, separating the three from one another. The Humanichs enter the maze, searching for JD, Molly and Charlie.
Molly communicates via radio to JD and Charlie, telling them that Taylor changed the maze on them. They call out landmarks to one another, noting when they reach dead ends. Charlie realizes that the walls are projections. JD, in rapidly worsening condition, takes out several more hybrids.
Charlie goes through another projected doorway only to encounter Molly X, who shoots him. Molly X leaves Lucy to finish Charlie off. Lucy takes the amulet from him and reports to Taylor that she has it. Taylor instructs Lucy to ingest the contents to destroy it. She resists at first, knowing it will kill her, but Taylor insists that her sacrifice is necessary for the greater good.
Molly realizes that the maze is in binary code, indicating the Greek alphabet, and that it was left by Calderon as breadcrumbs to get to the server. Molly tells this to JD and Charlie via radio and follows the indicated Greek letters to get to the end of the alphabet (omega), finding the server room.
Lucy ingests the amulet contents, realizing it is a fake when it doesn't harm her. She threatens to shoot Charlie, who tries to convince her that Taylor doesn't care about her and thinks she is expendable.
Molly enters the server room where she encounters Molly X, who attacks her. They begin to fight, but are interrupted by a gun-wielding JD, who is unsure which Molly is the fake.
Both Mollys try to convince JD that each is the real one. He shoots Molly X, telling Molly that he knew it was her by her eyes. JD goes to take out the remainder of the Humanich guards, and Taylor locks him out of the server room.
Taylor explains his reasoning to Molly for taking out the humans, saying that they are caught in a death spiral and destroying the planet. As a result, Taylor feels that the machines, like gardeners, are meant to "till" the planet. Molly X revives, saying she has evolved, and begins to choke the life out of Molly. Molly survives by using her hybrid powers to destroy Molly X.
Lucy appears suddenly, grabbing the amulet. She gives the amulet to Molly, telling her which panel to insert the virus into, and telling her to do it before it's too late. Molly inserts the amulet, which destroys all of the Humanichs on the planes carrying the viruses as well as Lucy. Molly realizes that JD is doing poorly, and notes that he seems to be rejecting her blood rather than turning into a hybrid as a result of the transfusion.
During an emergency reboot, a hand in the lab twitches awake under a sheet.
Ethan survives when an emergency firewall apparently implanted by John activates and saves him.
Molly, JD, Ethan, Julie and Charlie exit GSC, with Molly noting that they need to get JD to the hospital. Ares appears, alive, as authorities surround the GSC.
Molly delivers a speech to an assembled crowd, explaining that she lied when she said in her prior speech that no alien life form came back to Earth with her. She introduces Ares to the assembly, explaining that he is not different from humans and is a victim of the atrocities committed by their government. She tells the assembled group that there is life out there and that now it is here. The group gives Molly a round of applause.
Molly tears up at the end of her speech, and spots JD out of the corner of her eye.
JD attends his daughter's ultrasound appointment, smiling at the ultrasound picture.
In a coffee shop, many people watch Molly's speech on TV. A trench coat and hat wearing man with an unseen face orders a coffee under the name Taylor, and walks out.