Manhattan is the latest branch of a bank to receive the calling card of the Architect, a master robber who got away with three earlier, similarly bloodless hold-ups. Peter sort of clears himself and gets jailed Neal his ankle device parole back, but on a trial basis for both of them. Neal proves the security insufficient and works out the likely identity of the Architect, squeaky clean but bored and arrogant wall Street mogul Edward Walker. Catching him proves harder, his easily seduced secretary and an inside accomplice the keys. Meanwhile Mozzie helps Burke keep track of Neal's mental recovery and discovers the mysterious music-box's disappearance from evidence.

Neal goes undercover as a political "fixer" in order to bring down a corrupt politician.

FBI stumbles upon a new con-artist who is using Neal's styles to steal paintings from the museum.

For the first time ever, Mozzie must turn for help to the FBI, via Neal, desperately worried when the person of his affection, waitress Gina De Stefano from a local diner, disappears. Mozzie uses cryptic clues, often references to book texts, left by Gina to find and rescue her. Neal got Peter also on the alert, and it turns out she has a boyfriend, petty thief Tommy Barnes, long on the FBI's radar, who works for a big fish, Colombian 'cigars' dealer Navarro, who actually abducted Gina to get Tommy to return what he stole. Neal concocts a convoluted plan to catch Navarro and liberate Gina, involving ID gay Devlin but compromised as Mozzie spooks Tommy.

Neal finds himself working with Sara Ellis an insurance investigator who has it for him. He and Peter are helping her find out who has possession of Japanese bonds. They believe that man named Mr. Black who they believe is a courier whom the one is possession of the bonds wants to move them. So they come up with a plan for Neal to take his place. When he meets the contact he gives Neal a gun and brings him to the apartment of Ellis, whom he has to kill. When they fake her death, she along with Peter and Neal try to find out who wants her dead.

The arrest of a jewel thief puts Peter and Neal, who poses as fence-collector, on the trail of the laundering agent, adoption lawyer Donovan, who extorts adoptive parents with fake claims from biological mothers to pay off his gambling debts with a Russian mobster. Mozzie breaks into Sara's apartment and captures Kate's recording, soon recovered by Sara Ellis and her detectives searching Neal's apartment. After teaming up with the mob, Peter and Neal arrest Donovan. Sara promises, after finding out what happened to Kate, to help Neal with his investigation. The recording reveals that Kate called an unidentified person shortly before the jet exploded, so Neal and friends target whoever was on the other end of the phone.

Peter's quality evening plan for home-cooking stew or his wife again falls out as Peter's big boss needs him to chaperon Neal as only person skilled enough to help John Deckard's US Marshalls team catch FBI agent Jack Franklin, presumed to have gone rogue. Peter wants to give his former colleague, suspected of getting rid of key witness Rebecca Vidal in a mob case, a fair chance. Neal proves himself an even better salesman at the luxury cars dealership where she works, and tracks her down. Franklin comes and surrenders his weapon to Peter, whom he convinces to have been set up by Deckard, the real witness program traitor. Cued by Neal, who even talks the boss out of turning them in, they dodge the fiends, seeking shelter with Mozzie, and go after proof against Decjard, and Neals sets a trap for both him and his mob boss.

Wesley Kent's microchip firm's head researcher Joseph Hayes is murdered by poisonous overdose, presumably on account of his revolutionary invention. The duo goes undercover, but due to his major, Peter now gets the cushy alias of pampered rating agency accountancy expert. Neal joins the competitive junior executives in a cubicle, but gathers no less information there. After Mozzie discovers Peter has the music-box, he must accept to continue the Kate investigation officially, with a stuck-up FBI agent as equally unamused partner.

Neal orchestrates an elaborate con to bring himself face to face with Kate's murderer.

When Peter is suspended by the FBI for a crime he didn't commit, he is forced to run a sting with Neal and the gang to catch Mozzie's shooter, and clear his name.

With the mastermind behind Kate's death uncovered, Peter and Neal explore their pasts to gain answers.

The desperate UN ambassador to the UN called a favor from the FBI to help his estranged son, a human rights activist, who was arrested in Burma and faces an atrocious sentence for ruby theft. Neal, who grew up fatherless, convinces reluctant Peter to condone dodgy means against the Myanmar junta. After finding out the true master thief, Andrew Collins, Neal has an irresistible fake made by Mozzie as a trap for greedy Burmese ambassador Kyi, but it can only work if they find a way around the inviolability of his diplomatic pouch confided to his assistant Suu.

An old friend of June's late husband, Ford, has returned after a stint in prison. Neal suspects the man is dangerous and fears for June.

When Peter is kidnapped by an old nemesis, Neal must race against time and defy the FBI to save him.

Peter and Neal assume each other's identities to uncover a collusion scheme.

Neal gets closer to finding out the truth about Kate's death.