Bill and Jeannie are in the city walking with Baby Adam and go by a power substation. Bill points out that Jeannie is good with the baby and assures her that she would be good with the ones they have as well. As she wonders what kind of world they'd be bringing children up in, an explosion rocks the power substation behind them.
After sending his wife out of town, Bill goes to the office where John and his tac teams are coordinating the hunt for Stanton. There have been five attacks on power substations in the last week and the power company workers will have protectors in place within a few days. Rachel tells them that according to the intercepts, Stanton will be launching a major assault in the next few days. Rosen looks at the board with his files on Stanton and realizes that in two days it will be the 150th anniversary of Stanton's first "death" and resurrection. Bill wants to pursue the lead on the electronic shipments, figuring that they're critical to Stanton's plan, but John believes that pressuring Stanton's organization is the better option. Meanwhile, Rachel tries to find Skylar and have her analyze the components that they have. Rosen wants to probe Mitchell's mind and see what other memories Stanton stored there, and asks for permission to move him from Binghamton to a psych hospital in New York City. John hesitates and Kat offers to go since she won Mitchell's trust. Rosen objects, saying she doesn't have enough experience, but John agrees to move Mitchell and let her accompany the convoy.
Stanton and his Alpha operatives go to an underground bunker inside of an abandoned National Guard armory. Scipio informs his superior that the doctors will soon be there and the medicines are stockpiled. He reports that Vince is still working on Skylar and Stanton, impatient, says that he'll talk to Vince. As they walk through the bunker, Stanton tells the others that it was Danielle's idea and that she wanted somewhere that their people could come to during the transition.
At the office, Rosen visits Bill, who explains that his wife was traumatized by the nearby explosion. Rosen says that he wants to take the fight to Stanton, but Bill interrupts when a call comes through to him from Washington. Before he answers, he realizes that Rosen wants to run their operation outside of the DoD, and tells him that they all need to be working together. Rosen agrees and leaves, but then tells Cameron that they can't count on Bill. He assures Cameron that Bill's involvement isn't critical and hopes that he doesn't get in their way.
That night, Kat and Mitchell are driving the convoy van with Mitchell inside. Scipio tosses incendiary grenades at them, driving two of the vehicles off the street. As John and his men open fire on Scipio atop a parking garage, Stanton's operative Jeff Kowalka rips the van door off and leaves with Mitchell. When Kat tries to go after him, Scipio blocks her path with another incendiary. However, someone shoots him with a tranq dart. By the time Kat, John, and the tact team get to the roof of the parking garage, Scipio is gone.
Jeff takes Mitchell to the bunker and a doctor removes the nullification chip. Stanton sends the others away and takes Mitchell's hand so he can experience the memories he stored in the Alpha. However, he realizes that none of the memories are there and Mitchell confirms that Rosen nullified them through drug treatment. He admits that for the first time in years, he feels like himself.
Rosen meets Nina, Cameron, and Rachel at a warehouse where they've taken Scipio and chained him with his hands on his own chest. They remove the batteries from their cellphones so Gary can't trace them and wake Scipio up. When Rosen warns him that he's going to kill millions and can still make amends, Scipio doesn't care, boasting that he killed his parents and that Rosen is 20 years too late to try and change his attitude. Nina tries to push Scipio into telling them about Stanton's plan only to discover that the same Alpha that put blocks on Burton's mind has done the same thing to Scipio. All she can get him to admit is that there are hundreds of shipments like the one they intercepted. When Nina can't get through Scipio's resistance, Rosen has Rachel prepare to administer psychotropic drugs to their captive.
When Bill comes in the next morning, Kat worries about how she messed up and lost Mitchell and Scipio. He tells her not to worry and to focus on Stanton's assault. She tells Bill that she hasn't talked to Nina and Rachel, and they confirm that Cameron isn't in his office. As they talk, Gary comes in from the hospital and explains that the doctors chased him out for being a nuisance. He explains that when he took the taxi over he noticed the GPS and decided to ping the chip in Skylar's arm that she uses to communicate with her wasp drones.
Skylar is in an apartment making a new device as her daughter Zoe looks on. While she works, Skylar complains that she hears a buzzing noise and scratches at her left forearm. She says that the phone must be ringing but Zoe points out that they don't have a phone. Skylar starts to find that odd, but is interrupted when Vince comes in with groceries. He asks if she's making progress with the device and admits that he could be in trouble if she doesn't finish it, and Skylar assures him that she'll get it done. Vince offers to take Zoe for a walk to give Skylar some time to concentrate. However, Vince goes to see Stanton instead. Stanton orders him to pressure Skylar into finishing the device immediately so he can complete his project.
Nina finally asks for a break when she's unable to get past Scipio's block. Rachel warns the others that Scipio's blood pressure is reaching dangerous levels and that Nina is exhausting herself. She wants to call in the experts but Rosen and Cameron insists that they can't trust the DoD since Stanton has infiltrated it. Rosen has Rachel prepare a stimulant and Nina explains that it's for her, not Scipio. Nina still fails and Rosen says that he has another idea.
At the office, Gary informs Bill that Skylar is ignoring him. When he tries to check the others' phones, he discovers that they're shut down. Kat reports to Bill that she found a tranq dart at the parking lot and that it had Scipio's blood on it. None of John's team had tranq guns and Bill starts suspecting that his teammates are up to something.
As Skylar welds a piece with a miniature blowtorch, she hears the buzzing sound again and jerks, dropping the torch. When she picks it up, she burns her hand but realizes that it doesn't hurt. Skylar scans her arm and finds one of her own chips in it, and realizes that she doesn't have her drone wasps. Zoe suggests that her mother call back whoever is buzzing her on the chip.
Gary gets a signal from Skylar.
Cameron brings in Megan Bates, another of Stanton's operatives and leaves her with Scipio. She asks if Stanton is still at the house and Scipio assures her that she hasn't broken, but finds her curiosity puzzling. He admits that he missed her and says that his memories of their time at a cabin in the woods have helped him resist the interrogation. When Megan says that the mountains were pretty, Scipio head butts her and yells that Megan has allergies and hates the mountains. Nina, staggered by controlling Megan, staggers out. Cameron goes over and beats Scipio until Rosen finally stops him.
Rachel and Cameron take Nina away and Scipio taunts Rosen, asking how it feels to have his daughter betray him. Rosen fills a syringe adrenaline and asks Scipio if he's ever considered how his victims felt when he burned them to death. He then tells Scipio that once he injects the adrenaline, the Alpha's power will activate automatically and Scipio will burn himself. Scipio refuses to talk and Rosen gives him the injection. The Alpha burns himself and screams in pain. Rachel and the others are in the office, and Cameron stops her when she tries to intervene. He brusquely tells her to cover her ears if she doesn't like it and Rachel leaves, saying that she can smell Scipio's flesh burning.
When Vince comes back in, Skylar starts making a device from parts in the kitchen. He tells her that the apartment is safe but she turns the device, a flamethrower on him. He simply stands and stares as the room flickers. Zoe screams and Skylar tells her to run, and then runs out after her. However, Zoe vanishes and Skylar discovers that every hallway leads back to Vince's apartment, where he warns her that things could get much worse if she doesn't cooperate.
In a dingy apartment, Vince monitors Skylar and Zoe, who are drugged unconscious and lying on beds. He mutters about how things could get much worse if Skylar doesn't cooperate.
Stanton calls Mitchell into his command center and prepares to put more of his memories into the Alpha for posterity. When he takes Mitchell's hand, Mitchell recites the memories out loud, saying that he's going to change the world and that it's a shame that so many people have to die.
Scipio finally tells Rosen what he wants to know, but Rosen hears the DoD pull up outside. Rachel tells them that she called them in and Rosen says that it's okay before leaving with Cameron. Nina stays with Rachel as Bill and the others burst in. They secure Scipio and Megan and Nina tells Bill that Rosen got what he needed. Bill tells Rachel and Nina to come back to the office with them, much to Kat's surprise. He points out that even though they lied, he still needs them to find Stanton. Gary pulls up in a taxi and tells them that he's tracked Skylar's signal. They follow the signal to the apartment and break in. When Vince tries to run, Bill knocks him out and frees Skylar and Zoe. Skylar explains that when she refused to work for Skylar, he captured her and forced her to work for him building a device while under Vince's influence. Gary sees the sketches of her work and asks what they are. Skylar, recognizing them, says that they're the end of the world.
Cameron and Rosen go to the address Scipio gave them and discover that Stanton has prepared the bunker in preparation of a disaster. The two men find the control center and discover a map of the U.S. with red flags in many of the major cities. Rosen tells Cameron to take the information to Bill and the others while he stays behind to do what he has to. Cameron gives him a gun and reluctantly leaves.
As they return to the office, Rachel tries to apologize to John about betraying him but he tells her they'll discuss it later. Skylar tells the group that she made a mini-stim which hooks up to a light or a computer screen. It will enhance an Alpha's powers but give normal humans lethal seizures, and Stanton has made millions of them. Cameron arrives and shows them the map, and they realize that Rosen stayed behind to kill Stanton. Bill agrees to send a few people to the bunker but tells the team that their primary focus has to be on finding and destroying the mini-stims.
The power & light company workers finish putting in the protectors at the substations.
Rosen finds Mitchell inside the bunker and hears him muttering about Stanton's plans to change the world and kill millions while watching from "a god's eye view." As Rosen tries to work out what that means, Stanton and his operatives leave the bunker. Rosen tells Mitchell to hide for two days until he can return and then goes outside. Stanton and his team have already left, but Jeff has stayed behind. As Rosen goes to a SUV to pursue them, Jeff opens fire with a submachine gun. Rosen ducks into the SUV for cover and Jeff tells him that Stanton still wants Rosen alive. Police sirens sound in the distance and Jeff leaves before they can arrive, while Rosen realizes that one bullet hit him in the stomach.