Michael Westen is a spy who receives a "burn notice" while on assignment. Spies are not fired, rather they are issued a burn notice to let the agent know their services are no longer required. Penniless, Michael returns to his roots in Miami where he freelances his skills to earn money. First up, Michael helps a man clear his name after valuable pieces of art and jewelery are stolen.
Michael prevents a man from committing suicide, whose son suffers from a heart condition. He had lost his savings in a scam after investing in a "miracle drug" for his son, so Michael decides to get him his money back. Meanwhile, he has to deal with an explosion at his place and his brother in jail.
Michael, under the alias of Miles Parker, is hired by Scott Chandler to investigate strange activity - log-ins at odd hours, unusual computer activity and telephone bugging - at an art gallery. But after being attacked by the the gallery's receptionist, Michael finds himself working against Chandler. Meanwhile, Michael needs to find the person who planted the bomb at his loft, therefor he turns to arms dealer Seymour for help.
Barry enlists Michael's help in tracking down his money-laundering client list, which has been stolen by a vicious thief. Michael goes after the thief, only to find that there's a lot more to the situation than he realized. Fiona tries to be supportive of Michael's efforts to reconnect with the intelligence community, but she and Michael find that their differences on the subject may not be reconcilable.
International fugitive Simon is loose and Michael's on the run from the FBI for his role in Simon’s escape. When Simon confronts Michael and threatens to blow up a Miami Beach hotel, Michael must call on his friends and an old enemy to help him avoid disaster and put Simon back in the dark hole where he belongs.
Before Sam Axe teamed up with Michael and Fiona, he was Commander Axe, U.S. Navy SEAL. The Fall of Sam Axe tells the story of how Sam went from respected Naval Commander to the man of mystery we've come to know on Burn Notice. On what will turn out to be Sam's last military mission, he is sent to the jungles of Colombia to investigate claims of a vicious terrorist organization known only as the "Espada Ardiente" (Flaming Sword). His mission: to determine whether U.S. military aid is necessary to deal with the threat. But when he arrives, things are more complicated than he'd imagined. He receives word that the rebels have targeted a small civilian clinic deep in the jungle. Sam must now save the clinic's doctors and patients from certain death. However, nothing is as it seems and the Espada Ardiente may not be the biggest threat Sam Axe faces.
After the CIA denies his request to see Fiona, Michael calls upon his old Mentor, Tom Card. Michael offers help on a mission to take down a notorious drug cartel if Card can get him visitation privileges. In prison, Fiona is targeted by a ruthless gang leader, and must turn to a new friend in order to fend them off.
When Agent Pearce learns the identity of her fiancée's killer, she enlists Michael's help to seek revenge. Things get complicated, however, when they discover the man is under protection as a CIA asset. Meanwhile, Fiona seeks out a well-connected prison smuggler to find out who was behind an attempt on her life.
Michael's deal with the CIA sends him to the Dominican Republic to infiltrate a terrorist organization headed by an old contact. Sam, Fiona, and Jesse try to move on with their lives, but are drawn back in when someone starts asking questions about Michael's whereabouts. Maddie tries to get custody of her grandson.
Michael meets a former Russian operative who now works as part of Burke’s mysterious organization. In order to get out of Cuba, they’ll have to outwit a bloodthirsty counterintelligence expert who’s locking down the island. Strong convinces Fiona to help Michael’s mission by making her an offer she can’t refuse.
Michael and Fiona pose as hackers at a malicious programming syndicate in order to steal information for Sonya. But Michael’s life gets complicated when working with Fiona again brings back painful memories. Meanwhile, Sam and Jesse help Barry track down a former girlfriend in exchange for falsified documents.
Michael finally meets with the head of the organization he’s been assigned to dismantle, but things get dicey when the leader drugs him at gunpoint in order to learn his deepest secrets. In danger of exposing his cover, Michael soon realizes that in order to protect his future... he'll have to face his past first.
When Michael discovers an old friend digging up secrets that could expose his cover, he must decide just how far he will go to protect the mission. Meanwhile, Sam and Jesse are thrust in the middle of a street war involving a decade-old murder after Fiona’s boyfriend is targeted by a coldblooded gang member.
Appearing as a Season 2 Easter Egg, "Boom Notice" is a behind-the-scenes fake episode focused on boom mic operator "Fred". Featuring crew playing parts that may seem somewhat familiar.