Rachel, Nina, and Cameron are tracking a Red Flag operative, assassin Isaac Hale. He's working with another Alpha to track someone through the streets of New York City. He's the only lead they have after several of the terrorist organization's leaders have disappeared in the last week. As a couple arrives at a pawnshop, Isaac confronts them and demands what the woman, Danielle, has. The Alpha concentrates and the nearby flowers wither as he unleashes his power of advanced necrosis, the same power he used to kill the three MK scientists. Rachel hears them and leads her teammates to them as Isaac corners his two victims. He kills the man, Will, and Rosen arrives in time to see Danielle. He calls to her by name and she tries to flee, and he tells Nina to push Danielle and stop her from running. However, Danielle uses her own Alpha ability to grab Nina and hit her with a wave of sad emotions so that she can get away.
As Cameron and Nina search for Isaac, Nina explains that she knew that Rosen had a daughter, but not that she was an Alpha with the ability to transfer emotions. Rachel loses Isaac Bill arrives at the office and discovers that Gary is coordinating efforts for the team. When Gary points out that Bill is on medical leave, his friend says that since the infarction, his system has normalized. He's been using his time off to check on Stanton Parish, the name that Griffin gave him. He figures that Stanton is on Rosen's cloud drive and asks Gary to check it.
Gary spots Danielle at the Baltimore Hotel and tells Rosen her location. Rosen goes there and pounds on Danielle's door, begging for her to come out. She finally does and says that she doesn't want him there, but Rosen insists on helping. As she walks away down the hall, Isaac finds them and approaches. Rosen tries to get her away but they run into a dead end. Isaac concentrates on the two of them and insists that neither one of them has to die. Cameron arrives and shoots and kills Isaac before he can kill them.
Back at the office, Rosen gives Danielle a medical and wonders what drugs that she's taking this time. She admits that she's taking an anticonvulsant and insists that it's better than the drugs he proscribed for her. Danielle asks him for a prescription so he can get her out of his life, but Rosen refuses to let her walk away again. When he asks why Isaac was chasing her, Danielle claims to have no idea who Red Flag is. Kathy Sullivan arrives and privately informs Rosen that they know that Red Flag is going to strike the next day at 7 a.m. When Rosen worries about his daughter, Sullivan tells him to compartmentalize and not let his personal issues interfere with their case.
Bill is talking to his wife and taking pills when Gary arrives with a report on Stanton Parish, who was on Rosen's cloud drive. He supposedly died in 1974 and worked with MK Ultra, and wrote a manifesto for the Alpha cause. Bill asks Gary to find out everything he can.
Rosen tries to talk to Danielle about what happened and offers to help, insisting that he loves her. Dani points out that he has always treated her like a test subject, and that Will would do whatever he could to help her. Danielle finally gives him a necklace with several fake rubies on it and explains that's what Red Flag was after.
Gary goes to see Anna at a greenhouse. After her Alpha bodyguard searches Gary, he sits with her and she takes his hand. Anna then asks him about the quote from Parish that he sent her and where he got it. She warns him that Parish is a dangerous man and Gary shouldn't be asking question. Gary realizes that she's talking about him in the present tense and Anna tells him that he has to go. Her bodyguard leads him away over Gary's objections.
Rachel examines the necklace while Rosen talks with his daughter and insists that he's a different person than he was 15 years ago. Danielle points out that he still manipulates people and notes that whenever her mom got angry at him for locking himself up with lab work, he'd come to Danielle and ask her to bring his wife a cup of tea. She points out that her empathic contagion would calm her down, and that he knew what she could do for three years before she moved out with her mother when she left Rosen.
As Rosen walks away, Bill catches up to him and explains that he and Gary found something huge. Gary admits that he talked to Anna despite their orders and confirmed that Parish is still alive. He did a search by face and confirmed that Parish was a Russian scientist working on their version of the MK Alpha program. Digging further, Gary confirmed that Parish was alive since the Civil War. Bill figures that the shapeshifter was sent in to wipe the files on Parish and covers his tracks to hide the fact that he doesn't age.
After analyzing the fake rubies, Rachel explains to the team that they were synthetically made and are a perfect storage medium. Putting them together makes a jump drive and Gary reads the encoded data, while Bill points out that it's the same code that Anna uses. Gary deciphers them and confirms that they're GPS coordinate for Highland Mills, 60 miles away. Rosen points out that there's a time, the time of the big Red Flag event. There's a final message, "We're not the problem but the solution," the signature phrase of Parish, and they realize that he's called a Red Flag meeting.
Rosen calls and passes the information onto Sullivan. As they prepare an attack on the location, an abandoned brick factory, Gary worries that Anna will be there and could be hurt. Sullivan says that they'll use non-violent methods initially, but she can't guarantee anything. Cameron offers to go in with the assault team and Bill insists on going as well despite Rosen's protest that his heart isn't yet ready for the stress.
The next morning, Rosen goes over Parish's manifesto as the others prepare to move out. Danielle asks her father if Red Flag is responsible for Will's death, and says that if they are then she hopes they take in the group. He admits that he knew about her ability and tried to use it to save a marriage that he had already ruined. When Danielle wonders what he wants her to say, Rosen tells her that he doesn't expect her to say anything. Meanwhile, Gary calls his mother and tells her that he won't be coming home because his friends need him. He tries to assure her that Bill will protect him, and has kept Gary from taking a bullet in the past.
At Highland Mills, the assault team watches as Anna and the other Red Flag people arrive at the factory to meet with Parish. Gary insists that he should go in and persuade Anna to give herself up. Nina talks to Cameron, noting that he appears comfortable as an assault soldier, and he tells her that he has a love-hate relationship with the military. He starts to tell her about his feelings if something happens to him, but Nina says not to jinx it.
The meeting starts and Rachel confirms that Parish and a dozen of the Red Flag leaders haven't arrived. She listens in and tells Rosen that those that there have begun the meeting and plan to go public. Rosen figures that it's a setup and tells Sullivan that Parish is using them to capture the peaceful wing of Red Flag. Sullivan is glad to capture who she can and dismisses Rosen's concern. He admits that they're not innocents and Sullivan orders her people in. Nina insists on going in even though she's wearing a mask that blocks her ability.
Sullivan's people fire gas in and move on the terrorists. Gary runs in and Rosen goes after him. Meanwhile, some of the Red Flag Alphas fight back. Cameron goes up against a woman capable of deflecting his shots with her knives. Another one burns Bill with an acid touch, putting stress on his heart. Bill manages to take him down, while Cameron fights his Alpha. He realizes that she's like him, but she says that she's better and knocks him out.
Anna's bodyguard finds Gary and grabs him, and Nina runs up, rips off her mask, and tells the Alpha to sleep. Once he does, Gary goes with the soldiers to find Anna. A knife comes spinning out of the gas, killing one soldier. Sullivan authorizes return fire while Gary calls for Anna. The Red Flag operatives return fire and one of them accidentally shoots Bill in the bulletproof chest, stunning him long enough for the burning Alpha to grab him. Bill has no choice but to amp up to save his life.
Gary finds Anna and discovers that she's been shot dead. When one of the soldiers tries to lead him away, Gary grabs a baton and beats him repeatedly. Assuming that Gary is a Red Flag terrorist, the soldier prepares to shoot him and Rosen arrives just in time to stop him.
Later at the office, the team meets and Gary insists that Anna shouldn't be dead. He blames himself for not saving her and comments that Rosen doesn't know everything. The others say that they can't continue doing what they have been, fighting against their own kind. Rosen says that they're a team and that what they've done, they've done for the right reasons. He assures them that they have nothing to be ashamed of. Bill starts to object, but Sullivan arrives and asks to speak to Rosen in private. She says that it's a win and promises to give Rosen whatever resources he needs to find Parish if he exists. When she suggests they bring Danielle on the team, Rosen tells her not to talk about his daughter. Rosen starts to walk away and Sullivan tells him that the DoDo heads want Rosen to meet with them in a closed-door session and give them his input.
At home that night, Rosen tells Danielle about what happened and she realizes that he doesn't have all the answers, and that she likes him better that way. He apologizes for what he put her through and says that she's his daughter, not his patient, and wants her to do her thing to him so he knows what she's feeling. Danielle reluctantly takes his offered hand and Rosen winces at the strength of her emotions. Once she's done, he admits that he doesn't know what to say and Danielle says that it worked.
Later, Danielle goes to bed and Rosen swims in his pool. When he looks up, he finds Stanton Parish waiting to talk to him. He assures him that he came alone and Danielle is fine, and asks Rosen how it feels to be living his dreams. Rosen protests about being used to eliminate Parish's opposition in Red Flag. Parish explains that he prefers to walk in the shadows and points out that Rosen and the government don't want the existence of Alphas revealed to the public any more than he does. He explains that he has complete control of his mind, perfect brain-body connection, and tells Rosen that humanity will soon become as elevated as he is. When Rosen says that they have nothing in common, Parish says that there will be war between Alphas and humans within the next two or three years, and that he can give Rosen understanding of Alpha biology. In return he wants Rosen's help, but Rosen says that people died and he's done enough. Parish says that he'll come along and leaves.
Rosen prepares to leave for Washington and asks Cameron to check on Danielle from time to time. He then addresses the DoD, warning them that the violent wing of Red Flag is still at large. They offer him more tactical teams and assure him that they can confine many more prisoners at Binghamton. Rosen objects, saying that the abuses there can only thrive on the dark. The DoD is unaware that Rosen is secretly transmitting the entire meeting worldwide via one of Skyler's gadgets, a pen-camera. Finally he declares that all Alphas exist, and that they are their friends and spouses, sons and daughters.
Parish watches the broadcast and admits that things have become complicated. Danielle is with him and says that she warned him.
Sullivan realizes that the meeting is being broadcast live and has Rosen taken away as he says that complete transparency is the only way to avoid the war that is coming.