In San Francisco, Winston and Chance are waiting at a sidewalk café, and Winston complains that their new client is a paranoid nutjob who has been having them run all over town before he's sure that he can meet them. As they talk, a man tries to park and argues with another driver. He backs into a parked car, and his own car explodes. They figure the man is their client and run to help. As the flames spread toward the leaking gas tank, Winston and Chance get the man out just in time before his vehicle explodes. They confirm that he's alive, and Winston has to admit that he might have been wrong
At the hospital, the ER doctor confirms that the man is okay except for head trauma, and is suffering from retrograde amnesia. The only treatment is patience and therapy, and it could take years for him to recover his memory. They go in to talk and Winston notices he's been given John Doe as a generic name.. He doesn't know who they are or who he is. They explain that he was the target of a car bomb and offer to help.
Chance and Winston take John Doe to the office. Ames nicknames him J.D. and figures he's a crook running a scam. Ilsa is surprised and unhappy to discover that Chance and Winston forged her signature to make her J.D.'s legal guardian. She wonders why they didn't go to the police, and Winston notes that J.D. was very specific to keep the cops out of the matter. Ilsa reluctantly gives in, and then hands out their paychecks.
J.D. insists to Ames that he's a good guy, but she doesn't believe it. Guerrero arrives to inform them that J.D. isn't on file in any fingerprint or facial recognition database, and the car is rented under an assumed name. The car's navigation system shows that J.D. was holed up at a hotel for the last few days. Guerrero needs to look at the debris to possibly identify the bomber. When he discovers he's received a paycheck, he complains to Ilsa, insisting that he never takes checks because they can be traced to him. She tells him to deposit it and pay taxes.
The police arrive and Ilsa refuses to lie to the police. Lt. Broward and Lt. Delgado arrive, and Broward admits they haven't been able to identify J.D. When they ask to see J.D., Winston objects and it's clear the two men have a history. Winston refuses to turn J.D. over until a judge issues a ruling. Ilsa leaps in and assures Broward that they'll inform him if J.D. remembers anything. Once Broward and Delgado leaves, Winston explains that Broward is a crooked cop. He was never able to prove it, and it cost Winston his job and his reputation. Chance figure that Broward wants J.D. for a reason, and once they learn that, they can take Broward down.
Chance, Winston, and Ames take J.D. to the hotel where he was staying. They find newspaper articles about various crimes, and J.D. insists that he must be a good guy. Ames and Winston aren't convinced, and Ames locates a key hidden behind an unused ironing board. J.D. doesn't remember it, and Chance says they should go back to the office and check the footage on the security camera.
Guerrero poses as a bomb squad member and goes to the site. He claims that he's been chasing the bomber for months and intimidates the other squad bomb squad members into backing off while he checks out the car. He calls and tells Chance that whoever set the bomb was an amateur. Chance notices some bikers with the Mongrel gang showing up at J.D's motel room... and that Ames and J.D. are still inside.
The bikers open fire and Ames gets J.D. on the floor. Winston opens fire, while Chance makes a Molotov cocktail and sets the nearby cars on fire to drive them off. Broward and his men arrive and order Chance and Winston to drop their weapons. He takes J.D. away, saying that he's under police protection. Winston tries to stop him, but J.D. insists that he wants to be with the police for his own safety. As Broward takes him away, Guerrero calls to say that he interrogated a Mongrel. The biker said that they were hired to take out J.D.'s protection. Winston figures that Broward hired them so he'd have an excuse to take custody of J.D. Chance agrees with Winston, and Ames is the one who warns them to slow down.
As Broward drives J.D. away, he tells J.D. to drop the act, and says that they're old buddies. When J.D. still says he's ignorant, Broward says that he's no longer useful and prepares to kill him. Chance and the others arrive, shoot out Broward's tires, and take J.D. Broward warns that he's still a cop, and he'll have Winston and his team arrested and put away for good. Winston and Chance are unimpressed.
A little later, Delgado and his men arrive at the agency and inform Ilsa that they have a warrant for her arrest, and that of the rest of the team. She stalls and calls Chance and Winston, who explain what happened. She figures that she can let herself be arrested, but Winston reminds her that Broward's men are crooked. Chance tells her to take off her high-heeled shoes.
Delgado and his men break in and search the office. He finds her shoes beneath the desk and figures that she's somewhere there. Meanwhile, Ilsa has hid in the space above the elevator. She takes it to the ground floor and gets out, and then calls Chance again. He tells her to get to a bus stop, and he'll have Guerrero pick her up.
As they drive across town, Ames notices that J.D. has a pen from a storage unit, and they figure they key they discovered will unlock a door. They go there and discover that J.D. had a safe house. There are files and a computer, but the system has been wiped clean. Ames finds a van filled with millions of dollars. Winston tells her to back off, and they find J.D.'s ID, which identifies him as David Jarecki. J.D. doesn't recognize the name and Chance calls Guerrero and asks him to identify Jarecki's name. Guerrero identifies Jarecki as the most talented money launderer on the West Coast.
Ilsa is at a bus stop avoiding her new "neighbors" when Guerrero picks her up. She wants to use a credit card to make some purchases, and Guerrero explains that if she does then she can be traced.
J.D. tries to resolve himself to his newfound identity, while Chance and Winston figure that Broward was using Jarecki to launder his dirty money. Winston says that he needs to go to his old place while Ames searches the place. Surprised, Ames wonders how he can do that, and Winston tells her that he trusts her.
Winston takes Chance to the home of his ex-wife, and Chance is surprised to learn that Winston was married. Chance says that Winston never told him. Michelle greets them at the door and figures they're not there for a social visit. While Winston recovers the evidence that he kept there, Chance and Michelle avoid talking to each other. Winston finds the box with the evidence, and tells Michelle that he's finally going to bring Broward down. She says that some people never change. Winston has the bank account numbers, but they're anonymous. However, they can use J.D.'s records to identify them. The police pull up outside and Michelle says that she'll cover for them as they get out the back.
At the safe house, J.D. calculates the exact amount of money based on the size of the pile. Ames realizes that he's a "Rain Man," and they're going to go to Las Vegas to take advantage of his skills. Winston arrives and Ames explains that J.D. has a photographic memory, so there are no records. Furious that his life's pursuit is shot, Winston grabs J.D. and Chance pulls him off. Winston figures that it's all over now, but Chance insists that he has something now: the rest of his team. Chance figures that they need to give Broward Jarecki.
Guerrero and Ilsa pick up Ames, and Guerrero gives her the keys. He takes Ilsa to the bank. Meanwhile, Chance takes J.D. to the police station in and tells him to pretend he has his memories back, and then get the off-shore account numbers. Ilsa will bankroll the $2 million they need to convince Broward that J.D. is legitimate.
Ilsa tells the manager that she plans to place her funds in his bank, but needs him to overlook the 24-hour hold on major transfers. He soon agrees and takes Ilsa's ID. Chance brings J.D. in and then identifies himself to the police and invites them to arrest him.
As Guerrero and Ilsa prepare to leave with the money, Ames notifies them that the police have arrived. Guerrero tells her to keep them out, and she smashes his car into a parked car to distract them. The manager, Paul, arrives with Ilsa's welcome packet, and she asks if he has a back way out. He's more than glad to oblige.
Chance and J.D. are brought to Broward and his men, and J.D. says he'll give Broward two million dollars in return for his freedom. Chance claims that he's been hired to protect J.D. and his money. Broward wants to see the money first, and Winston transfers the funds. J.D. shows Broward that he has the money, and asks what account he can send it to. Broward insists on typing it in himself, but hesitates before hitting transmit. He asks J.D. to name the bar where they conduct business. When J.D. claims he knows the name of the bar, Broward says they never met in a bar. J.D. says that it's a setup, but offers Broward the money at the safe house. Broward agrees and J.D. apologizes as he's taken away. When Broward's men prepare to dispose of Chance, he takes all four of them out. The legitimate police come in and arrest Chance.
J.D. takes Broward to the safe house and shows him the money. Once he's satisfied, Broward prepares to kill J.D. Winston comes in behind him and holds Broward at gunpoint. Broward figures that he's got nothing, but J.D. memorized the number that Broward types on the keyboard. Broward attacks Winston, who quickly subdues him and takes his badge away. He leaves with J.D. as the police arrive.
Later, Ilsa pays Guerrero in cash, but he wants additional money for reimbursements. As he goes, Guerrero reveals that he bought her a pack of paper: the same paper the Department of the Treasury prints money on. Chance tells J.D. that if he cooperates with the investigation and turns over the money, the police won't prosecute him. However, he'll have to go into the Witness Protection Plan in case any of his other clients come after him. Chance and Ames then reveal that they traced the explosives, and discovered that J.D. bought the bomb. He planned to fake his death and leave with the money, but it went off early. J.D. is disgusted with himself, but Ames and Chance tell him that he has a rare opportunity at a second chance.
Winston goes to see Michelle and apologies for his obsession. He tells her that it's over, and figures that their marriage would have turned out different if he had caught Broward eight years ago. Michelle tells him that if it hadn't been Broward, it would have been someone else, and that Winston's focus was never on her. She tells him that they both deserved better. Winston walks away.
Later, Winston returns to the office and tells Chance that it didn't go well, and he admits that he gets obsessed with his work. When he insists that he told Chance he was married, Chance points out that he's a lousy liar, but a great cop. They share a toast over Winston's success in bringing Broward down.