With a few months left on his four-year sentence, criminal mastermind Neal Caffrey escapes from maximum security prison to save his relationship with his girlfriend. FBI Agent Peter Burke, the man who had chased him for years and had finally caught him, is called in to track him down. He easily finds Neal at his girlfriend's apartment, deflated and defeated. She has completely disappeared. Back in prison and with four years added to his sentence, Neal decides to make a deal with Agent Burke to help him in finding other master criminals. The deal is made and Neal is released, with a GPS ankle monitor, of course, into the custody of Agent Burke. The uneasy partnership proves a success and Neal becomes an official FBI consultant, living large, to Agent Burke's astonishment and frustration, in a wealthy widow's guest-room. Neal, also, secretly brings in an old friend to help him find his girlfriend.
It's Fashion Week, and while Neal is enjoying himself, Peter is less enthusiastic about the legion of beautiful women that has descended on Manhattan. Things get worse when one of those beautiful women is witness to a murder. Peter and Neal interview a model named Tara who watched as the notorious Israeli counterfeiter Ghovat killed one of his business associates. Peter thinks Ghovat is in town with something to sell, and fashion week gives him the perfect cover. But how to find this man they call "The Ghost?" Neal has an unorthodox suggestion: throw a party. Judging by Ghovat's proclivity for gorgeous women and glamorous scenes, it's only a matter of time before he shows up. With Elizabeth's event planning expertise, Peter and Neal plan a lavish affair designed to catch the eye of the counterfeiter. Neal and Tara work the party, keeping an eye out for Ghovat, while Lauren Cruz, a beautiful, whip-smart agent transferred from the Violent Crimes Unit, keeps an eye on Neal. The trap is set, but the wary Ghovat slips through the FBI's fingers.
Mob baron Burrelli asks FBI's help to solve the theft of his parish church's Bible, from 17th century Naples, where it would have worked several miracles. Neal assumes it may be meant for healing, as it's very hard to fence, having contacted expert Fiametta, who points out it's actually a breviary, not a Bible. Neal and Peter soon find the vagrant who was hired to steal it but robbed himself, and suspect a link with the nearby murder of rivaling mob family member, which is alas assigned exclusive to a jealously rivaling FBI agent from organized crime.
Burke's wife brings a friend of hers to see him. She tells him her husband a soldier is being sought for smuggling gold into the country. Burke tells her that her husband should turn himself in which he does but claims to be innocent. But Burke says the evidence against him is irrefutable; his fingerprints and hair were found in the gold. The soldier claims that someone from the State Department tried to get him to bring the gold in but he refused. With Neal's help they deduce that the evidence against him may have been planted. And it takes them to a news reporter who interviewed him who was also overseas at the time the gold was being prepped to be sent. So they think the reporter and State Department man are involved and try to prove it.
When a painting is stolen, Peter and Neal are tasked with finding it. They get a lead on the thief, they set a meeting but something goes wrong and the man disappears. They try to find him using info he uttered at the meeting. Later a curator from a museum in Europe claims that the painting was stolen from the museum years ago and when the painting is recovered, he expects it to be returned to him. Neal talks to the owner and learns that her family has a connection to the painting, which makes Neal wonder who the painting really belongs to.
Peter is looking for an FBI agent who went under cover to get something on an Asian criminal who appears to have vanished. He sends Neal under the guise of being a high roller playing Pai Gow. While in the midst of the operation, there's a raid and Neal is aided by the hostess. When they're alone she disengages Neal's wire and reveals that she's an Interpol agent. She wants Neal to make sure the FBI doesn't interfere with an operation in exchange for information about Kate. When asked he doesn't tell Peter anything. But Peter checks her out and learns that the reason she gave Neal is a lie. Neal has to choose who will he side with.
Neal Caffrey has no alibi for the robbery from a Manhattan fashion house's safe of the world's largest pink diamond, which was replaced by a masked man resembling him with a synthetic one bearing his initials. Peter Burke has nothing to prevent Neal being jailed by a hostile agent from OPR, the FBI's internal affairs branch. Neal however escapes, helped only by Mozzie, 'hides' at the Burke home invited by Elisabeth and sets out to prove the only other logical suspect, Tumblane, faked his alibi and was hired by a third party.
Neal and Peter go undercover to take down a corrupt group of Wall Street brokers. If the mission fails, Neal's deal with the FBI could be negated.
Peter Burke accepts to help David Sullivan and other victims of a plot in which people are forced to take and pay off a second mortgage due to wrong foreclosures. Neil finds out those are all signed by federal judge Michelle Clark. Mozz helps him collect evidence from her chambers, but Fowler helps Clark turn the table on Burke who tried to trick her into bribing him. Neil must turn the tables on both the fiends.
When June's granddaughter Samantha needs a donor organ, Peter and Neal stumble on the trail of illegal organ trade. Neal approaches Dr. Wayne Powell, the ringleader, posing as an 'approachable' doctor. That leaves only Peter to seduce his female cahoot. Finally an elaborate 'Indian' trap is set.
A female thief escapes from the home of a murdered art collector, posing as a victim. Neal helps bothersome Burke, who invites himself to his luxury home while his apartment has state of the rat HiFi installed, identify and find her. They work out her latest robberies are after a historically priceless set of imperial Chinese jade elephants, a matter of diplomatic interest, but find setting a trap unusually hard.
An old rival of Neal's issues a challenge to re-create a rare bottle of wine owned by Ben Franklin.
When the daughter of a man Neal once robbed, is kidnapped and the kidnapper is a man whom Neal worked with and betrayed, will only deal with Neal. So the FBI agent in charge of the kidnapping takes possession of Neal and sends him to meet with the man. When Peter talks to the father, he realizes that the man wants Neal but before he could warn him, he's grabbed. He wants Neal to help pull a job. Peter tries to find him. Neal gets word to Mozzie what he's been doing who tells Peter who figures out what the man is doing.
Alex Hunter finally teams up with Neil to steal the music-box, which she located in the Italian consul's safe, doubtlessly obtained illegally. Pete smells a rat but is kept at a distance, as the plan requires entering a witness protection relocation to Canada, arranged by dirty agent Garrett Fowler. An explosion changes everything.
