Rachel, Cameron, and Nina trail Isaac Hale, the Alpha who murdered the MK scientists, as he works with another Alpha to track someone through the streets of New York City. They figure the Alpha finds the target and Isaac kills them. The other Red Flag agents have gone to ground and Isaac is their only lead. The tracker finally spots a couple, Danielle and Will, as they go to a pawnshop to get her money for her fix. The tracker leaves and Isaac closes in on the couple and demands that Danielle turn over something. He uses his necrosis, killing the nearby flowers, and Danielle and Will run away. Isaac follows them and corners them in an alleyway.
Rachel hears them and tells Cameron. Meanwhile, Will attacks Isaac, who kills him with a touch. Cameron attacks Isaac and knocks him away. Rosen arrives and recognizes Danielle, who tries to run away. When Nina tries to push her, Danielle grabs her hands and Nina recoils in shock. Isaac escapes and Cameron goes after him while Rosen tells his team that Danielle is his daughter and goes after her.
As they look for Isaac, Nina tells Cameron that she knew Rosen had a daughter but not that she was an Alpha. She explains that when Danielle touched, her it felt like she lost her best friend. Rachel loses him in the crowd and they head back. Meanwhile, Gary is at the office coordinating efforts to track. When Bill arrives, Gary points out that he’s supposed to be resting after his recent infarction. Bill explains that it normalized his system, and he’s used his time off to check on Stanton Parish, the man that Griffin told him about who hired her. He wants Gary to check Rosen’s cloud drive to see Stanton’s name is on there.
Before Gary can agree to do it, he spots Dani on a security camera, going into a cheap hotel. He notifies Rosen, who goes there and knocks on doors until he finds her. She tells him that he doesn’t want her there and Rosen asks her to come with him. Dani refuses and walks away, and he goes with her and asks to help her. Isaac arrives and Rosen and Dani run. They end up in a dead-end and Isaac begins killing them, but Cameron arrives in time to shoot and kill him before he can finish the job.
At the office, Rosen checks on Dani’s vitals and learns that she’s taking anticonvulsanta to deal with the aftereffects of her power. Dani suggests that he just give her drugs and leaves, but Rosen wants to know why Isaac was chasing her. Sullivan arrives and talks to Rosen privately, informing him that they’ve been monitoring Red Flag communications and learned that they have something planned for 7 a.m. the next morning. She knows about Dani and tells Rosen to set aside his family business and focus on Red Flag.
Bill calls his wife and assures her that he’s fine to be back at work, but doesn’t tell her he’s taking pills for his infarction. Gary shows him the files from Rosen’s cloud drive, files that confirm that Stanton died in 1974, worked for the government on the MK Alpha project, and wrote a manifesto in favor of Alphas. Bill figures that Stanton is the key to everything and asks Gary to keep digging.
Rosen asks Dani what she knows about Red Flag, but she complains about how he has always treated her as a test subject rather than a daughter. She finally turns over a ruby necklace that she took from a man at a meeting, and figures that’s what Red Flag wants.
Gary secretly meets with Anna at a greenhouse. After her super-strong Alpha bodyguard searches him, Gary is surprised when Anna takes his hand. She then asks why he sent her a quote from Stanton and warns Gary that he is a dangerous man. Gary realizes that she’s referring to Stanton in the present tense but Anna tells him to leave before he can find out anything else.
While Rachel examines the necklace, Rosen tells Dani that he’s a different person. She doesn’t believe it and reminds him that he used to manipulate her by sending her to comfort her mother when she was upset with Rosen for locking himself away with his work. Rosen claims he didn’t know that Dani had an ability at that time but Dani reminds him that he knew three years before his wife left him and took Dani with him. Afterward, Bill and Gary tell Rosen about how Anna gave away that Stanton is alive. Gary did a search by face and found photos of Stanton going back to the Civil War. Stanton sent in Griffin to erase the files and keep his existence hidden.
Rachel works out that the fake rubies are laboratory-grown silicon and serves as storage medium. She shows the team that when they are properly assembled, they work as a flash drive. Gary reads the information and tells the others that the data is encoded using Anna’s language. He decodes some of it and finds GPS coordinates for the town of Highland Mills. The time of 7 a.m. given, indicating that it’s an invitation. At the bottom is a quote from Stanton’s book and Rosen figures that he’s called the meeting.
The team brings in Sullivan, who congratulates them on their efforts and confirms that the location is an abandoned brick factory. She prepares an assault team while Gary warns that they can’t hurt Anna. Sullivan says that they’ll do what they can to capture Red Flag rather than kill them, but insists that the terrorists will be neutralized. Cameron agrees to join Tactical and protect Anna, and Bill says he’ll go in with Nina and Cameron. When Rosen objects, warning him about the stress to his heart, Bill says that it’s the end-game and there’s no way he’s sitting it out.
Rosen goes over Stanton’s manifesto before leaving with the others. Dani comes in and wishes them well taking out Red Flag since they killed Will. He admits that he was right about using her ability to manipulate her mother and trying to save the marriage that he had ruined. When Dani wonders what he wants her to say, Rosen tells her that he just wanted her to hear it. Meanwhile, Gary calls his mom and tells her that he won’t be coming home, and assures her that Bill will protect him from any bullets.
The assault team arrives at the factory and watch as the Red Team members, including Anna and her bodyguard, enter the building. Gary wants to talk to Anna and get her surrender but Rosen refuses to let him go on ahead. As Cameron suits up, Nina points out that he’s comfortable as a soldier and Cameron admits that he has a love-hit relationship with the military. He starts to tell her something in case he doesn’t come back but she says not to say anything because it’s bad luck.
Rachel confirms that Stanton and a dozen of the Red Flag leaders haven’t shown up, and the others start the meeting. She informs Rosen that they’re talking about going public and telling the world the truth about Alphas. Rosen realizes that Stanton is setting them up to eliminate his opposition within the group and tries to warn Sullivan, but she isn’t interested in the difference and orders her men in to capture who they can. Nina dons a gas mask against the tear gas despite the fact that it blocks her abilities, and then goes in with Cameron, Hicks, and the DoD agents.
The DoD fires in tear gas and calls on the terrorists to surrender. When Gary realizes that Anna’s in trouble, he runs down to help her and Rosen goes after her. Meanwhile, individual fights break out. Anna’s bodyguard takes on the agents while Cameron fights a woman, Gabby, capable of blocking bullets with her knives. The two of them fight and she says that she’s like him, only better, and knocks him out.
Bill battles an Alpha capable of generating heat from his hands. After he’s shot in the chest and stunned, the Alpha tries to kill him and Bill has no choice but to amp up and knock him away.
When Cameron’s opponent kills a DoD agent, Sullivan authorizes the others to open fire on the remaining terrorists. Meanwhile, Anna’s bodyguard finds Gary and grabs him. Nina arrives in time to save her teammate, ordering the bodyguard to go to sleep. Gary searches for Anna and finds her corpse. When a DoD agent tries to pull him away, Gary attacks him and is almost shot by the DoD before Rosen stops them, but he can only watch as the remaining Red Flag members are gunned down.
Later at the office, the team wonders if they can fight their own kind anymore. Rosen tells them that they’re a team and what they’ve done, they’ve done for the right reasons. Sullivan calls Rosen away and informs him that it’s a win. She insists that they’ll get Stanton and offers Rosen everything he needs to do the job, including more Alphas. She offers him the services of Dani and he refuses to discuss it. Rosen doesn’t believe it and Sullivan tells him that he’s been invited to a closed-door session of Congress to give his input.
At home, Rosen talks to Dani and she admits that she’s learned he doesn’t have all the answers. She says that she likes him better that way and that he can’t imagine what she’s been through. Rosen admits that he never emotionally knew what it felt to be her and asks her to use her power on him so he can experience it first-hand. Dani finally takes his hand and lets him experience what he’s feeling, and Rosen admits that he doesn’t know what to say. His daughter tells him that if that’s the case, then it worked.
As Dani goes to bed, Rosen exercises in the pool and finds Stanton waiting for him when he’s done. He says that he came alone and Dani is fine, and asks how it feels for Rosen to be making his mark on history. Stanton insists that secrecy serves all of them: himself, Rosen to protect his team, and the government. He casually dismisses Anna and her people as troublemakers and Rosen analyzes him, noting that the downside of his immortality is a complete lack of emotional empathy. Stanton insists that he has moved beyond being an Alpha and has complete control of his mind and body. He aspires to have all of humanity elevated to his status but Rosen warns him that he won’t be manipulated. Stanton assures him that there will be war between Alphas and normal within the next 2-3 years, and that Rosen is close to knowing everything he wants about the biology of Alphas. He offers to get Rosen there in return for help with his plans. Rosen refuses but Stanton tells him to think about it and assures him that he’ll come around.
The team wishes Rosen well as he heads for Washington for the closed-door meeting. Gary gives him a pen from Klausworks and Cameron promises to look after Dani while he’s gone. In Washington, Rosen tells the committee that the leader of Red Flag is still at large. When the committee offers to provide him with whatever he needs and confine the Red Flag Alphas at Binghamton, Rosen clicks the pen on. He then condemns Binghamton as a clandestine prison hospital used to confine individuals without regard for their human rights.
At the office, the team watches as Rosen uses the Klausworks pen-camera to transmit his words to the entire world. Rosen points out that Stanton wants the Alpha phenomena kept secret just as the government does, and that that policy will lead to war. Sullivan realizes that the meeting is being transmitted live.
As Rosen speaks of how Alphas are among them and they are no different than anybody else, Stanton watches the transmission... with Dani. She warns him that it might happen and Stanton admits that things just got more interesting. Meanwhile, Rosen says that public knowledge of Alphas may be messy, but it will tell show everyone that it is time to open their minds and their eyes. Before he can finish, the committee has him taken away, ending the broadcast.