Fiona debriefs the president by phone on how the search for Molly Woods is going.
Molly, JD and Ethan drive back to the city with the virus-containing amulet.
Someone, face unseen, hangs themselves using a sheet.
Fiona and Lucy discuss history, specifically the mission to take out Osama Bin Laden; Fiona tells Lucy that that mission was accomplished while hers was not, and asks what she will do to accomplish her mission.
Ethan opens the door to Julie's apartment when Julie doesn't answer their knocking. They see Charlie hanging by a sheet from the ceiling fan.
At a street market, Terra, bleeding, runs into JD's ex-wife Dorothy and asks for her help because "they" are after her. Terra recognizes that Dorothy knew her father, Ahdu, and tells Dorothy that. After a moment of hesitation, Dorothy helps Terra get away.
JD and Molly get Charlie down, saving his life. When asked why, he tells them that he did it because Julie is dead. Ethan asks whether it's possible she is still alive, and Charlie explains that Lucy's plan was to torture him with never knowing what happened to Julie. Molly offers up the possibility of destroying the monster he created (Lucy).
Molly and JD tell Charlie about Taylor, and how he is the real enemy. Molly explains that the amulet is a self-replicating worm which will destroy Taylor's hardware. JD suggests blowing up the entire building since the server is highly guarded. Charlie counters that doing so would take out all technology. The three formulate a plan for a more surgical strike, that would avoid shutting down all technology (causing "Cybergeddon").
Ethan shows up at GSC headquarters and hugs both Fiona and Lucy, telling Lucy he missed her and telling Fiona that there isn't much time. Fiona takes Ethan away for ice cream and tells Lucy to monitor any of Ethan's communications.
Charlie, JD and Molly discuss how they sent Ethan in as a plant. Dorothy calls JD to tell him that she has Terra. JD goes to retrieve them. Charlie voices his concern and sadness that Julie is already dead and expresses hopelessness. Molly comforts him, encouraging him not to think of the worst.
Ethan tells Fiona about the entire situation with Taylor. He requests that they shake on it (like they do in movies) to be sure that there is a deal. After their handshake, Ethan tells Fiona that she can talk to Molly via special virtual reality glasses that allow them to seemingly appear face to face. Molly tells Fiona that she cannot escalate the issue with Taylor to the president and needs to help them take care of Taylor before he finds out that they know. Molly abruptly disengages their communications before she can be traced by Lucy and a GSC worker back at headquarters.
JD brings back Dorothy and Terra, who was shot by the Humanichs in broad daylight. They treat her wounds. Molly tells Charlie that it is now up to Fiona.
JD and Dorothy discuss how Kelsey is doing with her pregnancy. JD tells Dorothy that if anything happens to him, he took out a life insurance policy. Dorothy resists hearing that, and JD tells her it is just a precaution. Molly overhears the conversation.
Lucy tells a GSC worker to expedite the new shipment of Humanichs. Fiona discusses the drone log check with another GSC worker, and the fact that it is unclear who ordered the strike. Another worker tells Fiona that the virus containment unit was breached, and that a virus was stolen. Fiona realizes that the stolen virus is one of the earlier versions that kills not only hybrids, but humans as well.
JD's friend Ray finds JD rifling around in the Ray's garage. They discuss how JD is a fugitive. JD tries to recruit his friend to the cause. Ray agrees, in exchange for a sum of money.
Molly tells Dorothy it is kind of her to help them with Terra. Dorothy expresses happiness that Molly is well, after her near brush with death. Molly mentions that she is luckier than Ahdu. Molly points out that Dorothy still loves JD. She tells Dorothy to go tell JD how she feels.
Lucy reports back to Taylor that Fiona can no longer be trusted. Taylor reveals that he knows, because he knows Fiona checked the drone logs. Taylor confirms that they are not going to eliminate Fiona yet, while she is still useful.
Molly, JD, Ray and Charlie discuss the plan to get the power grid down and get into Taylor's server grid. Charlie confirms that they have five minutes to get to the grid once the system is down, before the backup boots up. Charlie tells Molly that she needs to memorize the grid maze, which she does instantaneously.
Fiona and a GSC worker wonder how there is no footage of the breach and who might have the virus.
Lucy coordinates the dispersal of the virus via Humanichs to various major cities around the world, by plane.
Dorothy tells JD that she and Kelsey need him and tries to convince him not to go on the suicide mission. JD realizes that Molly put her up to this, and Dorothy tells JD that Molly loves him. JD tells Dorothy to go home and take care of their daughter and grandchild for him. Dorothy tells him he is a good man, kisses him, and leaves.
Terra explains to Molly that Ares came for her. They discuss how there are good and bad humans, just as there are good and bad hybrids. Molly tells Terra that in the end, kindness and compassion will save them all, not violence and anger. Molly tells Terra that she will ask her to do something to help set the scales right.
JD interrupts, confronting Molly about putting Dorothy up to trying to talk him out of the mission. JD brings up his prior military service, and how he was accused of walking away from his war. Molly counters that it wasn't his war, but JD says that the fight they're currently fighting now is his war.
Molly is interrupted by contact from Fiona via virtual reality glasses; she explains that Lucy sent a dozen Humanichs to deliver the human- and hybrid-killing virus by plane. She tells Molly that Molly and her group must move on Taylor now, because once Fiona orders the planes shot down, Taylor will be alerted that they are on to him.
Ethan vents to Richard his robot that he is worried Julie is really gone, and that Molly is on a dangerous mission. When Ethan goes to get Richard's charger, he finds Julie's charging station and smiles.
Fiona orders the power shut down.
JD and Ray pose as GSC maintenance workers to get into the facility. As Fiona shuts the power off, JD and Ray convince a security guard to let them in to take care of a malfunctioning cooling system.
Taylor switches the back up server on immediately. Fiona panics, while Lucy eyes her suspiciously.
As the lights switch back on, JD and Ray realize they have to abort the mission and run off. They are surrounded by security guards who shoot at them. Molly and Terra use their hybrid powers to stop the security guards, and they all flee by car.
Molly tries to communicate with Fiona to tell her to shoot down the virus-carrying planes, but is intercepted by Lucy. Lucy then mimics Fiona's voice to tell the president that everything is fine. We see that Fiona and the rest of the GSC human workers have been killed.
As they drive away, Molly comes up with an idea to get back in: she and Terra need to find Ares. She points out that if JD goes with them, Ares will definitely not help them. JD reluctantly agrees to let Molly and Terra go on their own, provided that they meet back at Julie's apartment in one hour.
JD explains the hybrids to Ray, and Ray elects to opt-out of the mission, given that he doesn't want a super-computer to come after him.
Back at the house, Charlie tells Ethan that the mission is over and was a failure. Ethan tells him it is not over, and shows Charlie Julie's charging station, explaining that the charger has Julie's coordinates. According to the coordinates, Julie is at the Humanichs lab.
Lucy and the Humanichs activate a Humanich replica of Molly. They send the replica over to get information out of JD. The replica tricks JD into telling her that Molly has the amulet, and then shoots JD.