The sixth season of the American television spy drama Burn Notice premiered on June 14, 2012 on the cable television channel USA Network.
Michael looks all over Miami for Anson, but does not have very much time to find him. An old nemesis, Agent Bly (Alex Carter), interrogates Fiona after she is arrested. Bly tries to get Fiona to give up information on Michael's involvement by saying he died in a truck explosion. Fiona sees through the deception and stays with her story that she acted alone at the British consulate. Michael, Sam and Pearce corner Anson at a chemical plant. As Michael is about to bring him in, Anson reveals a dead-man switch that will trigger a bomb in the plant, and Michael allows him to escape. Michael warns the others, who make for the exits. Pearce and a colleague make it out in time, but Sam stays behind to free a hostage that Anson had chained to a pole. After the plant explodes, several seconds pass before it is revealed that Sam and the hostage got out alive. Meanwhile, Jesse and Madeline deal with a paranoid Army Ranger patient of Anson's, whom the latter sent to Madeline's home in order to buy time. Pearce alerts every major agency about Anson, putting him on every watchlist.
To gain visitation rights, Michael offers his services to the CIA Agent who trained him personally: Tom Card (John C. McGinley). Michael and Jesse initially intend to team up, selling a cover as corrupt DEA Agents wanting a piece of the action of a cartel with the ultimate goal of moving the drug shipment. But Michael notices that Montero (Anthony Ruivivar), the second-in-command of the cartel, is represented by a lawyer that would recognize Michael from a previous encounter, forcing Jesse to do the job alone with only outside help from Michael, Sam and Card. In the end, Jesse gets the second-in-command to become a cooperating witness and ring in a major bust. This huge a victory allows Michael to see Fiona. While the others take down the cartel, a fellow incarceree gang leader goes after Fiona because she disrespected her. Fiona fights and overpowers the cellblock queen known as "D.B." during a fire in a cell, earning respect in prison. Afterwards, Fiona is washing dishes with a new friend. This friendship is shortlived as she tries to drown Fiona, but fails. Fiona learns that the girl was ordered to kill Fiona, or the girl's sister would die. Meanwhile, Michael's brother Nate (Seth Peterson) returns to Miami, stating that his marriage has fallen apart.
Having learned that she has been targeted for murder, Fiona attempts to learn her would-be assassin's name. She befriends Ayn, who supplies black market goods to the prisoners. Ayn wants Fiona to arrange for the guards to be locked out of the cell block in order to knock her new competitor out of commission. Fiona does so after creating a makeshift explosive device. Meanwhile, Pearce gets Michael's team to help her take down the man who killed her fiancé years ago. The man, CIA asset Ahmed Damour (Faran Tahir), has a hard drive full of valuable information that protects him. Michael, Jesse and Pearce accompany Ahmed on his vacation cruise, dose him with a drug that replicates the symptoms of meningitis, and quarantine him. Sam, Maddie and Nate go to Ahmed's home impersonating a medical team, to convince Ahmed's son Sharif that he is in danger of infection. They eventually recover the hard drive, rendering Ahmed expendable. Michael visits Fiona in prison, where he learns the name of a guard who is part of a plot to kill her.
Michael, Sam and Jesse head to the Everglades to track the guard trying to kill Fiona in prison, but find the man dead at the hands of Rebecca (Kristanna Loken), the burned CIA agent now on Anson's payroll. Rebecca takes Sam as a hostage, forcing Sam to creatively get a message back to Michael and Jesse, who eventually rescue him. In the end, Rebecca reveals she has only been following Anson's orders to keep her brother alive, and she becomes an ally for the team. Meanwhile in prison, Fiona has to do another favor for Ayn in order to get two inmates who are trying to shiv her thrown into solitary confinement. This involves retrieving a special package on the outside for Ayn, but with Michael and the team gone, Fiona can only call on Maddie.
Tom Card offers Fiona a deal to become a CIA asset, which will get her out of prison and protect her from extradition, in exchange for helping the Agency bring down her old arms dealer, Greyson Miller (Wayne LeGette). Before he can carry out Card's mission, Michael must first protect Rebecca's criminal brother, Trent, from a mob boss (Rick D. Wasserman) who believes Trent is responsible for his father dying in prison. Through an elaborate ruse, Michael manages to convince the mobster that Trent is not the one who sold his father out. Finally, Michael meets with Greyson, who is then captured. However, Fiona remains jailed until Anson is found. Rebecca reveals that she knows where Anson will be in the future.
Fiona is about to get released from prison but an agent from MI6 tries to prevent that from happening. Sam and Barry get trapped in a house on the beach. Despite Barry suffering multiple gun wounds, Barry and Sam escaped the beach house alive. Michael, Jessie, Pierce, and Nate traveled to Atlantic City to capture Anson. Michael and his team staked out in a motel room and Nate almost blew their cover twice. Michael, in anger, tells Nate to leave Atlantic City so he would no longer be a distraction from the team. Nate, now separated from the group, sadly prepared to leave Atlantic City when he received a call from Michael saying that Nate was closer (in distance) from Anson as the rest of the team. Nate in response, located Anson, confronted him, and incapacitated him. Nate then proceeded to hold Anson at gun point (while standing behind Anson) and took him outside. Michael, Jessie, Pierce and the rest of their team then showed up on the seen and prepared to arrest Anson. Micheal, Jessie, and Pierce began to walk towards Anson and Nate when an unknown assailant fired one bullet from a sniper rifle at Anson's chest. The bullet penetrated through Anson's chest and went straight into Nate's body. Anson is killed instantly while Nate died moments later in Michael's arms as Pierce, Jessie, and several pedestrians who heard the gunshot looked on. Michael returned to Miami where he informed Madeline about Nate's death, who immediately broke down in tears. Later that day Fiona is released from prison and Michael and Fiona hug. Michael told Fiona, who did not know about Nate's death, that he needs her more than ever.
Sam agrees to help Evan (Brando Eaton), the son of his girlfriend Elsa (Jennifer Bini Taylor), when he falls into trouble with a ruthless loan shark (Richard Burgi). Meanwhile, Michael and Fiona reconnect as they search for the person whom Michael believes sabotaged his last mission, and they discover that Rebecca has gone on the run. But with Michael hell-bent on avenging Nate's death, he must look past his emotions to get to the truth.
Michael intentionally gets arrested in order to help the FBI take down a vicious Boston mobster. Meanwhile, Jesse and Pearce team up to investigate a gun sale, but run into danger.
Fiona has to break into a heavily guarded safe to help out a CIA asset who has been investigating a black market operative. Meanwhile, Sam and Jesse track down a sniper and end up in a mercenary camp.
To get out of Panama, the team must hijack a plane, which puts them in the crosshairs of a vicious drug runner. Michael is forced to trust Tyler Gray, the man who shot Nate, in order to escape. Meanwhile, to hide the flight from Card and the FAA, Michael contacts Madeline and asks her to seek the help of a computer hacker.
The gang cook up a hijacking scheme in order to escape from Panama, while Michael tries to skirt a Panamanian drug runner.
A smuggler Fiona met in prison needs help taking on a corrupt detective. Elsewhere, Michael teams up with a former enemy to deal with an even bigger foe.
Moments after Michael killed his former mentor, Tom Card, a CIA heavy hitter, Olivia Riley, is already closing in. If the team doesn't want to be locked up or killed, they have to run now and never look back. But Olivia Riley isn't so easily duped, and while the team makes their escape, she captures Sam, planning to use him to find Michael. Michael, Fiona, and Jesse now have to put their escape on hold while they try to find a way to get Sam back.
Michael arranges to be captured by a Syrian intelligence officer in order to rescue an inept smuggler; Riley offers Madeline a deal in hopes of tracking down Michael.
Michael sets up a deal to sell a valuable piece of technology, but things take a turn when Sam is caught up in a risky robbery. Elsewhere, Madeline recruits Barry for a dangerous favor.
Michael seeks refuge in a warehouse when he's caught in the middle of a smuggler's attempt to get revenge on his former client. Survival becomes a challenge as supplies run low and the exits are blocked.
Part 1 of 2. Sam and Jesse are captured when the gang are ambushed while attempting to make their escape.
A group of assassins targets the gang, forcing Michael to go on the offensive in the Season 6 finale.