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.

Michael works with his old agency to go after the people who burned him in a case that leads the group to Venezuela.

Michael has to balance his new agency duties and helping a woman recover her cousin, who is one of many being trafficked into the U.S. by the Yakuza. Against Michael's wishes, Madeline becomes a critical component of the plan to find the girls.

Nate returns to Miami to seek Michael's help to go after a loan shark who's harassing a widow. The guys soon discover that the loan shark is not all that he seems, however.

The team searches for a super-computer to clear Barry's brother of a server heist.

Michael plays a key role in a CIA murder investigation. Meanwhile, the team helps a client who reminds them of Michael — a former army sniper who wants revenge on the men who put his sister on the hospital.

The CIA abandons Sam after he goes undercover with a heroin dealer while trying to recover a weapon. Meanwhile, Pearce continues searching for Max's killer.

Michael and Sam try to retrieve a boy from an armed compound. Fiona and Jesse babysit a day laborer.

Michael and Jesse go on an extraction mission on a Caribbean island but end up trapped there by mercenaries. Meanwhile, Fiona tries to get information out of an ex by doing a favor for him.

Fiona and Jesse work together for a pharmaceuticals magnate, but soon realize that he is hiding something. Meanwhile, Michael and Sam take on a bomb-maker involved in Max's death.

Michael goes undercover with a group of hijackers in order to assist Jesse with a security job, but he changes the plan when the hijackers take hostages at the airport. Madeline assists Michael by organizing the hostages and trying to lead them to safety.

Michael and Fiona pose as a wealthy couple at a South American resort in order to extract a bioweapons specialist. Elsewhere, Sam and Jesse try to trap Max's killer.

With convincing from Sam and Jesse, Pearce begrudgingly lets Michael take drastic measures attempting to clear himself of Max's murder. Meanwhile, Larry returns, having kidnapped a government psychiatrist, and insists that Michael help him with a job.

Michael and Fiona plan to abduct a hacker in Puerto Rico in order to obtain his software, but the man has several other enemies to contend with. Elsewhere, Madeline learns to retrieve information from the police under the tutelage of Sam and Jesse.

When gang warfare claims the life of one of Michael's childhood friends, he teams up with the victim's brother to entrap the gang in a weapons scheme.

Michael leads a rescue mission for a scientist abducted by an African warlord, while Sam and Jesse get in trouble during an undercover mission. Meanwhile, Madeline discovers that someone close to her is keeping secrets.

Sam has a surprise reunion with Beatriz, whose newspaper articles have made her the target of a murderous Russian spy.

Michael needs Pearce's help to get in touch with a prisoner from his past who has information on Anson. Jesse tries to help his old friend expose his corrupt boss, who uses diplomatic immunity to get away with dealing diamonds.

As the team reaches a breaking point with Anson and his sinister plans, Pearce puts Michael in charge of his biggest CIA mission yet.