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 ...
Tipped off by campaign official Dylan Ledding, the FBI suspects slick senator Gary Jennings of illegal campaign fund raising and having inconvenient witnesses eliminated by Robert Barrow. Burke poses as a bulldog agent who promises to dig until he makes the earlier rejected charges stick. Neil gets recruited with a fake Harvard wonder boy identity and proves himself by solving a non-existent problem of his own making which even Mozzie fell for.
Mozzie fears that the object of his affection has been kidnapped, and turns to Neal and Peter for help. For the first time, Mozzie must put his faith in the FBI - and when the rescue mission takes an unexpected turn, he is forced to step out of the shadows and into the line of fire.
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 leads Peter and Neal toward a much more heinous extortion case against adoptive parents. To catch the heartless mastermind, Peter and Neal dive headfirst into the world of high-stakes gambling to force the criminal's hand.
An FBI Agent is accused of selling witness locations during criminal trials, and the U.S. Marshals ask Peter and Neal for help tracking down the suspect. But when Peter uncovers the truth behind the plot, he must dive into the world of exotic cars and go on the run with his fellow agent until he can prove the man's innocence.
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. Neil 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.
Realizing the music box is part of the treasures Alex Hunter robbed from single ship, Neal lets Mozzie fake an FBI file so Brooks will enlist his help to investigate just that. They realize the musical code requires an expert, Akihiro, but he's found murdered later. Neal is found out having arranged the music-box being stolen and donated to a Russian action, then refuses to accept being 'benched' when the trail leads to rogue FBO agent Garrett Fowler, whom he presumes Kate's murdered. His excessive risks pay off.
Mozzie was shot by a hit-man but surgery saved him. Neal agrees to go by the FBI book to see the hit-man, soon identified as Julian Larssen, and whoever hired him caught and punished. Larssen is suspiciously easily arrested after the forgers help burn his known aliases except one, but somehow managed to plant false evidence pointing to Burke as the killer. That suffices for Peter's suspension from the FBI, leaving only Neal's ways.
Upon learning who is responsible for what happened to Kate, Peter wants Neal to tell him all he knows about him. But because it means revealing some of his past criminal acts, Peter tells him that for the next 12 hours everything he says is off the record. So Neal tells him of how a few years ago he first came to the city and how he first met Mozzie. Then how he later met the man, Vincent Adler of how he also met Alex and Kate. And of the con which first brought him to Peter's attention.
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.