The Alpha Team is on the hunt for Isaac, the Red Flag assassin who recently killed the early contributors to the Alpha program. Meanwhile, Isaac is hunting his own prey: Dr. Rosen's daughter, Dani, who is also an Alpha. Isaac finds Dani but the team kills him before he can kill her.
Back at headquarters, Dr. Rosen grills Dani about why Red Flag was after her. Turns out Dani stole a necklace from someone at a Red Flag meeting, but why is it so important?
Bill returns to work sooner than he should to follow up on a hunch: Maybe Stanton Parish (the name given to him by another Red Flag assassin) might be on the office's MK Ultra cloud drive. The hunch pays off and Gary follows up on it by going to see Anna, a member of Red Flag, who quickly sends him away after he mentions Stanton Parish.
As Dr. Rosen and Dani get reacquainted, they unearth many dark secrets and bad feelings between them. Not that they have time to explore their feelings since Agent Sullivan is breathing down Dr. Rosen's neck for results. Bill and Gary deliver those results by finding out that Stanton Parish is eternal and that he is the true leader of Red Flag.
Rachel uses her senses to uncover the fact that the necklace Dani stole is really a jump drive holding an invitation to the next Red Flag meeting. With Sullivan calling the shots, the team decides to raid the event and capture Parish.
At the rendezvous point, tension builds, especially when Rachel isn't able to detect any sign of Stanton Parish. When the meeting begins without him, Dr. Rosen guesses that Parish has set the DoD up to kill the assembled members of Red Flag-something Agent Sullivan has no qualms with.
As the DoD tactical team attacks Red Flag, Gary jumps into the fray to protect Anna, whom he still considers his friend. As bullet casings and bodies pile up on the warehouse floor, Gary finds Anna but he's too late-she's dead. Gary is so distraught that he attacks a tactical team member and almost gets himself killed. When the dust settles and Dr. Rosen tries to talk to his team, they are all doubtful and dissatisfied but Sullivan counts the raid as a win. So, too, does Stanton Parish who shows up unexpectedly at Dr. Rosen's house to invite Dr. Rosen to join forces.
Later, when Dr. Rosen is asked to address Congress about the "Alpha Situation," he surprises everyone involved by televising his speech-making the existence of alphas public for the first time. No one is more surprised than Stanton Parish who is actually in cahoots with Dr. Rosen's daughter.