Season 6 episodes
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With Sam's health rapidly declining, the team rushes him to the home of a shady, but discrete doctor.
You Can Run
Jason Bly reaches out to Michael with an offer: if Michael turns himself in to the CSS, Bly will spare him from Riley's increasingly lethal tactics and try to keep Michael's friends out of jail. But, Fiona hears about the arrangement, and refuses to agree to any plan that requires Michael to sacrifice himself.
Odd Man Out
Madeline's luck has finally run out and she's forced to go on the run with Michael and the others. But before anyone can go anywhere, they need buy black-market RFID chips to go with their falsified passports. With Calvin Schmidt's smuggling business in shambles, the only person who can provide the chips is Schmidt's bitter rival, Vannek.
Best Laid Plans
Michael needs Madeline to get in touch with Barry so he can throw the CIA off their scent with a false money trail, but Madeline finds herself in her own heap of trouble when she's arrested by Olivia Riley.
Down and Out
Olivia Riley begins putting pressure on Madeline to see if she'll accidentally lead the CIA to where Michael's hiding. With their enemies closing in, Michael and the team have to find a discrete way to get out of the country, so Michael seeks out an infamous smuggler named Calvin Schmidt (Patton Oswalt). But as it turns out, Schmidt already has his hands full with a Syrian ex-spy, who's wife he helped smuggle out of the country years ago. The ex-spy will stop at nothing for the opportunity to torture Schmidt for information about his wife's location, so before Schmidt can help Michael and his friends get out of the country, Michael will have to solve Schmidt's problem first.
Means & Ends
Tom Card orders Tyler Gray to burn down Michael's loft. Michael has no choice but to let it happen if he wants Card to continue believing that he and his team died in Panama. In hopes of turning the tables on Card, Michael uses Gray to find out what he's been up to.
In the summer finale, Michael completed his mission and captured Tyler Gray, the man who murdered his brother. But Michael's victory was short lived when he learned that the only reason Tom Card sent him to Panama in the first place, was to have him killed.
In the mid-season finale of season 6, Michael and the team are sent on off the books mission to San Miguelito, Panama to apprehend Tyler Gray, the man who murdered Nate Shortly after arriving, however, the team is ambushed by a group of Panamanian mercenaries under Gray's command. Michael and the others are forced to abandon their safe house, leaving them stranded without time to call for backup or the tools they'll need to finish the job. Nevertheless, Michael is undeterred by the odds against him and refuses to allow Gray to escape Panama alive.
Michael and the team trace the gun that was used to kill Nate to a mercenary group. To find out who within the group is responsible, Michael approaches the mercenaries as a wealthy executive looking to hire a private army, but Sam and Jesse have to take over when Michael gets roped into running point on a CIA mission involving the agency's newest asset-Fiona.
The FBI's investigation into Nate's murder has been suspended. Michael wants to continue the hunt for Nate's killer himself, but he'll need the FBI's file of compiled evidence first. Sam introduces Michael to a desperate federal agent who's willing to hand the file over in exchange for help finding a notorious gangster.
Sam's girlfriend complains that her son, Evan, has stolen a valuable piece of jewelry from her. When Sam takes Jesse to retrieve it, they find Evan in the midst of packing up to leave town. It turns out a brutal loan shark is threatening to break Evans legs unless he steals an 18-wheeler truck filled with black market liquor for him, which leaves Sam and Jesse with no choice but to help Evan with the heist. Things get more complicated when they learn the truck they've just stolen isn't filled with liquor, but something much more dangerous.
Michael has a lead on Anson's location and with Pearce's help, sets up an official CIA operation to apprehend him. If Michael captures Anson, he can finally secure Fiona's release from prison.
Tom Card (Season 6, Episode 2) has set the wheels in motion for Fiona's release, but the CIA won't help unless Fiona becomes their asset and aids in the apprehension of her arms supplier.
Under the Gun
Michael is trying to find out who used a prison guard to go after Fiona. He, Sam, and Jesse find the guard shot dead at his house... with Rebecca (Season 5, Episode 18), Anson's right-hand-woman, standing over the body. Rebecca takes Sam hostage as she flees to the Everglades, forcing Michael and Jesse to chase after them without help from the police or CIA.
Michael is granted permission to visit Fiona, but before he arrives, she needs to find out who's trying kill her. Fiona goes to the prison's black-market dealer, Ayn, for the information she needs, but it doesn't come cheap.
Fiona is in a federal prison and Michael's worried she may lose hope of ever getting out. Desperate to see her, Michael goes to the CIA officer who trained him, TOM CARD (John C. McGinley), for help. Michael hasn't forgiven Card for abandoning him after his burn notice, but Card is the only person he knows who can help him see Fiona. In exchange for Card's help, Michael agrees to help stop a Mexican cartel from gaining a foothold in Miami. Michael and Jesse pose as dirty DEA agents to get close, but when he's almost recognized, Michael abandons the mission, leaving Jesse to fend for himself.
At the end of Season Five, Fiona turned herself in to the authorities for the bombing of a British Consulate to eliminate any leverage Anson Fullerton had over her and Michael. Anson tried to force Michael to rebuild the organization that burnt him, but with Fiona behind bars, Anson lost all his leverage.