Someone goes on a killing spree at Synalock, an internet security company. Five victims are shot and three are stabbed. The mass murder appears to be premeditated and the unsub appears to be filled with rage. He might have run out of ammunition at one point and resorted to using a knife to stab people. A missing employee is the first person of interest, but he turns out to have been away at a Doctor Who convention. The CEO's murder was particularly violent, and he might have been the main target.
The unsub is trying to make sure his wife and daughter are safe. His father tries to speak with him, but the unsub accuses him of being an imposter. Later, he ties up both his parents and prods them for information about "Dorado Falls" before killing them.
The team finds Luke's parents' bodies in their home, and they his wife and daughter into protective custody. They suspect Luke, a Navy SEAL, might be suffering from PTSD. He had been in the same Navy unit as Werner, the CEO of the security company, but that was over six years ago. It has been too long for anything to be a trigger. Morgan notices Luke's car had been in a recent accident, and thinks maybe the accident caused the unsub's current erratic behavior.
Werner and Luke had been on a covert mission called Dorado Falls in 2000. Luke's estranged wife, Jenna, tells them that her husband Luke was usually pretty good at separating his work life and his home life; he compartmentalizes. Luke has kidnapped a Navy general, who may also have information on Dorado Falls, which has been identified as a ship. Luke blamed the general for replacing his parents and covering up Operation Dorado Falls. Reid suggests that Luke might have Capgras Syndrome, where someone believes that loved ones have been replaced by impostors. The car accident may have triggered this condition.
Luke wants to trade the general for his wife and daughter, Ally, but General Milgram claims he doesn't remember Dorado Falls at all. Luke says he remembers everything now, including the two children he had to kill on the ship because they were witnesses and couldn't be kept alive. Rossi calls Luke and offers to take the general's place.
Hotch and Morgan arrive too late to get to Luke; Milgram is alone. Now disguised as an FBI agent, Luke manages to sneak into FBI headquarters armed with explosives, and is right in the bullpen behind Rossi and the other members of the team. Reid tells Luke that his real parents are now dead and tries to explain the head trauma that is making him think everyone has been replaced. He doesn't understand; Luke just wants to see his wife and daughter.
Hotch gets Jenna and Ally on the intercom, and Jenna speaks with Luke about something personal only they would know about, their honeymoon. Reid tries to give Luke an explanation of what's happening to him, that his eyes and mind are making him think things that aren't true. Luke insists on seeing his family. Rossi tells him to close his eyes and put down the detonator, and they'll bring in Jenna. Jenna hugs him, and talks to him, telling him to keep his eyes shut.
Luke relaxes enough to allow Morgan to cuff him. However, Luke opens his eyes and panics when he sees Jenna's face, and he doesn't think it's his wife. He has to be taken away forcibly.
Meanwhile, Prentiss has to be recertified, and Morgan has been assigned to oversee the training, although he doesn't think she could fit in with the team anymore. He admits that he's nervous because he thought they had lost her. Prentiss promises to make it up to him.