The NSA puts out an armed-and-dangerous APB on Jake, using a phony rap sheet as cover. Diane isn't thrilled and even Beckett is skeptical about the idea, but Kyle insists they have no choice.
An amnesiac Jake wanders into a club in Philadelphia and finds a street-fighting club in the back. Jake takes on the three-minute challenge with the main fighter. After a bit of sparring, Jake takes him down with one punch and the club owner, Caesar, hires him on the spot.
While Jake continues to make money in the ring, Diane tries to track Jake's nanite signal and Kyle wonders if Jake is deliberately blocking the signal. Diane insists something has gone wrong and continues to home in on Jake's location.
Jake impresses Caesar with his computer skills after covertly interfacing with the system. He then goes to his apartment, gets into the NSA system and finds his file, which is flagged as Disavowed. The NSA picks up the hack and orders the local authorities to go in. They hear gunshots ring out, and then a report that they've found a drug ring since Jake redirected the signal. Diane bursts into a rage and Beckett puts her on leave, and Diane leaves with her tracking unit and a fix on Jake's location. Diane tells the NSA she's going to a spa but Beckett doesn't believe this for a second.
Jake is still fighting in the ring and winning as Diane tracks him down. She approaches him at a diner afterward and it's clear he doesn't remember her. Jake ends up covering Diane's bill when she can't use a credit card, and notices that she seems to know him. They end up eating dessert together as someone watches Jake, and Diane spins him a story; a thinly-disguised version of what's going on with Jake. Jake overhears the man outside and quickly gets away as Diane gets a cerebral scan on him.
Jake confronts the man in the car and it turns out he's working for Caesar. He asks Jake to solve a computer problem which he quickly does. It's the security algorithm of a safe holding $10 million in payroll. Caesar wants Jake to help them.
The NSA continues to get more info on Jake while Beckett figures out Diane is up to something. Diane contacts her assistant Fran and tells her that Jake has amnesia. Beckett and Kyle confront Fran who explains about the amnesia, but doesn't know where Diane is. Beckett threatens to bug the phones and orders Fran to cooperate.
After his most recent victory, Jake refuses to finish off his opponent and staggers out of the ring. Diane confronts Jake who says he wants to work and is developing a death wish, and she tries to comfort him. They kiss then end up in his bedroom but Diane realizes she can't although she always wanted to. The next morning Diane wakes up to find that Jake is already out of bed watching her, and wants for them to go off somewhere together. But before Diane can explain, he hears someone outside and finds out it's a man sent to bring him to Caesar.
Caesar talks to Jake and reveals he knows about the APB, and suggests Diane is working with the NSA. Diane calls Fran to try to work out a way to cure Jake's amnesia with a theoretical antidote when Beckett interrupts. Diane begs for a chance and Beckett gives her 24 hours.
Jake calls Diane to lure her out of the room, then goes through her files and laptop. She comes back and he confronts her about her secrets. Jake doesn't believe her offer of help but when she mentions Kyle he remembers his partner from the bridge. She tries to get through to him but he doesn't trust her. He leaves and goes to accept Caesar's job offer.
Diane has no choice but to call in the NSA while Caesar goes over the plan with Jake and his other men. The robbery goes off and one of the guards pulls off a robber's mask. When they plan to shoot the man so he can't testify, Jake sets off the alarm and disposes of Caesar and his men. He takes them outside where Kyle, Beckett, and Diane confront him. Jake says he remembers him and the guards confirm that Jake saved their lives.
Back in the lab, Jake goes over his record and wonders if he can live up to his file. As Diane prepares to give him the shot to cure the amnesia, he asks Diane who she wanted something to happen with: the current Jake or the Jake in the files. She admits he's her best friend and gives him the injection and he gets his memories back.