Fiona debriefs the government workers on what happened with the explosion. She tells them they should want revenge for what was done to them.
Molly and JD watch a news report stating that Tobias, accused of treason, died in a car explosion. Molly cries over the fact that Toby died, with JD noting that he died during the right thing. JD tells Molly that they'll find Calderon as Toby was planning to, and shut down everything themselves.
Julie cries as she watches Ethan pack up his stuff and leave, telling him she'll send over the rest of his stuff when he's ready. She tells him she loves him and Ethan replies in kind. Molly tells Julie that it's time to put the past behind them, and they hug, with Molly telling Julie she'll always be a part of both of her and Ethan's lives.
Fiona consults with the computer Taylor, who tells her that Tobias seemed to have been killed by an explosion from an outside source. Taylor suggests that it was a hybrid attack but Fiona wonders why the hybrids would attack Toby if he was supposedly on thei side. Taylor also insinuates that Fiona's own safety is at risk, saying he has "unorthodox" ideas for her security.
Molly, JD and Ethan return to the bunker to find Terra gone. Molly unearths a box of John and Calderon's old office stuff. Molly and JD discuss what happened between Calderon and John years back. Ethan plays with an old holographic chess set found in the stuff, noticing that someone else is remotely controlling the other side of the board.
Julie tells Fiona about Lucy having killed a human and how John's message was activated as a result. Lucy shows up and Fiona reveals to a startled Julie that Fiona has made Lucy her head of security. She defends Lucy's killing of Nate (calling him a hybrid sympathizer) and tells Julie that they must put aside their past misunderstandings for the greater good. She also tells Julie there will be changes to the Humanichs lab: Humanichs will be working there now, building other Humanichs, to meet the US allies' Humanichs production demands.
JD, Molly and Ethan try to communicate with whoever is on the other side of the board, using binary code. The person on the other side of the board gives them coordinates, and they all assume that it is to Calderon's location. Molly tells JD that she won't let him join her and Ethan on their field trip to Calderon's because she is scared that he will die if he does.
Molly tries to explain to JD that she believes her "dream" was actually a vision, a prediction of his death. Molly tells JD that she's lost too many people she loves and that she won't lose him too. JD tells Molly that she won't lose him and that it's his choice to go.
Back at the lab, Julie walks in to find the Humanichs working to build other Humanichs. In hushed tones, Julie tells Charlie about the conversation with Fiona and how Lucy told Toby she was answering to a higher authority. She explains to Charlie that he needs to get close enough to Lucy to swap out her network card so they can figure out where her orders and coming from and cut them off. Charlie and Julie stage a fight, allowing Lucy to oversee it.
Lucy tells Charlie that Julie doesn't appreciate him. Lucy tells Charlie that she's been promoted to the head of Fiona's security team. Charlie suggests that they celebrate, and they set a "date" to celebrate in the lab that night.
JD, Molly and Ethan drive to the coordinates given by the remote-chess player. They find a pay phone with no headset attached. Ethan finds a bunch of dead birds all gathered around one spot and they realize that there is an invisible security fence there. Molly types the numbers from the remote chess player into the pay phone and it allows the security shield to retract.
At the government agency, Fiona tells Taylor about Toby's suspicions regarding Calderon and how Julie also echoed the same concerns. She tells Taylor to monitor national security networks for him, and warns that they may not be the only ones looking for him.
JD and Molly approach a house inside the security perimeter, leaving Ethan in the car with instructions not to leave. A woman with a shotgun comes up on them and leads them with their hands up towards the house, keeping the gun trained on them. In the house, Calderon enters, holding a gun of his own. He tells them to handcuff themselves. Ethan flips on the brights in the car, and Calderon goes out to investigate. While the woman with the shotgun is distracted, JD knocks her out and takes the gun. While Calderon is distracted, recognizing Ethan and calling him by name, JD also manages to take Calderon by surprise and knock him out.
JD tells Calderon that they know he killed John Woods and probably Tobias. Molly demands the amulet that John told them about via Ethan. Calderon says he didn't kill John, and that he didn't even know John was dead until they confirmed it. JD expresses disbelief. Calderon says that everything they think they know is wrong and asks what they know about Taylor.
As they work on the decoy network card, Charlie expresses guilt about how they are tricking Lucy. Julie argues that Lucy tricked him too, but Charlie argues that they are the ones who took away her free will and forced a destiny on her. Julie expresses regret for how they handled the Humanichs project earlier. Charlie and Julie kiss, with Charlie noting they don't have time for regrets.
Calderon explains to JD and Molly how Taylor (a system designed with the purpose of preventing human extinction) seemed to rapidly develop a mind of his own, and suggests that Taylor framed him for the bombings. He mentions that Taylor was designed to make decisions based on what would protect the greatest number of humans. Calderon says that John had a killswitch to stop Taylor and that Taylor knew it and killed John. Molly realizes that the killswitch is the amulet. Calderon tells her that it disappeared when the government infiltrated his property.
Lucy joins Charlie for their "date" at the lab, where he's decked it out in a France-theme. Lucy wonders why he did all of this and Charlie says he did it to apologize for treating her like a machine, telling her that she's so much more than a machine. Charlie tells Lucy that he's been working on a side project, a neural sensitivity enhancer designed to give her more enhanced human experience. Lucy volunteers to be the beta tester, and allows Charlie to swap out her card. She kisses him.
Calderon explains that his mute companion, Frankie (the woman with the shotgun) is another Humanich-type robot, called a Sentient. He notes that Frankie's voice chip ran down a while ago, hence why she doesn't talk.
Molly and JD go outside to talk. She confesses that she's glad that the amulet doesn't exist because now she feels he won't die since there is no amulet. JD says that perhaps Calderon, who told them they could stop running and hang out at his house, has a point. JD suggests that they enjoy what time they have left, even if it's just for a night. They have sex.
Calderon, meanwhile, lurks around his house, locking Molly and Ethan out and approaches a powered-down Ethan.
JD and Molly discuss where they should escape to, but they are interrupted by Ethan shouting for help. They find Calderon doing something to Ethan. Molly uses her powers on Calderon, who expresses disbelief that she's one of "them." He explains that he just wanted to get Ethan's speech translator, because Frankie (his Sentient) has not spoken since hers wore out a while back. Ethan stops Molly from leaving, saying that he thinks he can help Frankie.
At the lab, Charlie and Julie work on detecting where Lucy's orders are coming from. They notice that the coordinates of the access signals are changing. Suddenly, the network card glitches and detects them, though Julie notes that they weren't supposed to be able to be detected. Lucy reawakens abruptly saying that she understands and will take care of it to an unseen/unheard entity.
Back at Calderon's house, Ethan gives Calderon his speech translator. Calderon puts it in Frankie, who wakes up and speaks to him.
The next morning, Calderon warns Molly that if she is a hybrid, the Humanichs are looking for her too. Calderon offers up a way to stop the Humanichs (though at a terrible cost) in order to repay Ethan's kindness by giving up the speech translator.
Taylor tries to convince Fiona to have the Humanichs patrol the streets for their own safety. Fiona resists, saying humans will feel as though they're being occupied, but Taylor continues to break down her resolve.
Lucy informs Charlie that the expedited order to ship out more Humanichs was approved, meaning that there will be Humanichs shipping out the very next day to all seven continents. Charlie immediately calls Julie to tell her. Julie tells him that they need to destroy the empty Humanich bodies asap, or they won't be able to stop the Humanichs occupation. She tells Charlie to meet her at the warehouse, with Thermite, so they can melt the bodies down. Lucy overhears.
Calderon is dropped off by Molly and JD near an ATM. In flashbacks, we see Calderon tell Molly about the virus that he and John created as a failsafe to shut down Taylor, which they began developing once Taylor was taken over by the government. They called it Einstein's Regret, after Einstein's noted regret of having signed a letter telling the president to develop an atomic bomb. Calderon notes that their other potential name for it was Zugzwang, after a chess move in which any move represents a loss for the player.
Charlie goes to meet Julie at the warehouse; instead he finds Lucy and no Humanichs. Lucy reveals that she knew what he was up to and that she hid Julie away. Elsewhere, Julie is trapped in a storage container with dwindling oxygen supply.
Calderon hands Molly the amulet that he took from the safety deposit, warning her that there may be no one outside of Taylor's influence at this point. He allows himself to be captured as Frankie watches sadly from a distance.
Back by the security perimeter, Molly tries to throw away the amulet but JD stops her, saying they have a magic bullet in the amulet and that they need to use it, regardless of the cost.