Michael asks Barry to track the Cayman bank account number he received from Derek Poole. While they are discussing this CSS agent Jason Bly shows up. He says can trace Michael to Barry’s illegal snooping, and he’s eager for revenge after Michael blackmailed and made him leave town. To make matters worse, Madeline has requested that Michael help her friend Paula, an assistant manager at a private bank; take care of a stalker named Prescott. Michael is followed by Bly to the bank, and sees Prescott arrive with four armed men and realizes too late that Prescott is actually a bank robber. Michael. All the bank patrons, including Bly and Michael, are taken hostage. Michael and Bly are going to have to work together if they are going to survive.

Michael and Bly decide to bury the hatchet after surviving the hostage situation. Michael gives Bly the blackmail folder in return for the information he needs about the Cayman bank account. Bly warns Michael that looking into the account set off a trip wire. Whoever owns the bank account knows Michael is coming.

Michael has identified the bomber who tried to kill him as Derek Poole so he contacts the arms dealer, Seymour, to help track him down. Seymour says he will help but needs cash to spread around. Michael is running low on money so he poses as a corporate espionage specialist to a job offered by Scott Chandler, a wealthy art dealer. Chandler found a bug in is office and is concerned that his competitors are hacking into his files. The job seems pretty simple until Michael finds out that the spying is being done by Chandler’s receptionist, Melanie. It turns out that Chandler represented Melanie’s artist father, J.D. Blake. Blake made threats to fire Chandler before he could sell one of Blake’s most expensive paintings. Mysteriously, Blake wound up dead and the painting was nowhere to be found.

In the mean time, Seymour helps Michael and Fiona kidnap Derek Poole. Poole tells them he is just a hired hand; the guy they actually after is his employer. All Poole can give them is a number to an account in the Caymans. The account number isn’t much, but it puts Michael closer to learning who wants him dead.

Sam asks Michael to meet with Sean, a former pro football player who is now a high school football coach in need of Michael’s services. One of Sean’s players, Corey Jensen, got into a fight with Felix Cole, the leader of a local gang of car thieves. Corey was projecting his sister and now Felix wants him dead. Michael and his team come up with a plan, pose as a rival gang and force Felix to leave town.

While this is going on Carla is pressing Michael to find the person who blew up his apartment and tried to kill him. Michael senses vulnerability, and he is actually a step ahead of her. Fiona finds the location of the bomber’s house, but walks into a fiery trap. Thinking Fiona has been killed, Michael is relieved when she walks back into his apartment and for an evening their passion is reignited.

After a very close call with an explosion at his apartment, Michael and Sam find themselves being chased by Carla’s men. The plan is to reorganize, but Michael finds himself coming to the rescue of his next client, Kenny, when he sees him step in front of a bus. Kenny had paid good amount of money to a doctor to help his sick son Jack, then found out the doctor was actually a scam artist.

Kenny’s story hits home with Michael so he agrees to help him get the money back he paid to the scam artists any way he can. Michael, Sam and Fiona capture and interrogate two low-level scammers in order to get to the mastermind of the operation, Rachel, a hardened thief whose specialty is targeting parents with sick children.

Their first plan backfires and Rachel flees, Sam worries that the job may be the only thing that is keeping Michael going. With the help of Fiona’s boyfriend Michael is able to locate Rachel’s house and get Kenny’s money back.

Michael has a face to face meeting with Carla, but gets another assignment instead of the answers he is seeking about his burn notice. The mission Carla gives him is to get a counterfeit copy of a high-tech security badge made. In the mean time, Sam introduces Michael to a new client, a woman who is being stalked by member of a drug cartel. The complexity of the job turns out to be greater than he originally anticipated, and the fact he must manage his job for Carla along with his mother’s insistence on attending counseling with her makes things even more challenging.

The season two premiere begins with Michael discovering that he has been recruited by the people behind his burn notice. Carla, his new handler, doesn’t waste any time making it clear that Michael will do as he is instructed or his family and friends will pay the price for his disobedience.

Michael’s new bosses want him to help Jimmy, a computer security tech, steal some data from a private security firm. To ensure cooperation they’re holding Jimmy’s family hostage. With Sam and Fiona’s help Michael comes up with a plan to get the data and save Jimmy’s family. This is Michael’s first step towards finding out who his new employers are and what their intentions are.

With assistance from Nate, Michael escapes the government operatives who just killed Philip Cowan and rescues Fiona from the heroin smugglers still after her. Meanwhile, Glen Harrick, an ex-special forces officer turned drug trafficker, has taken Sam captive and is using brutal tactics to force Sam to give up information on the people he is working for. In an attempt to keep Michael from trying to rescue him, Sam gets the beatings to continue and tries to get Harrick to kill him.  Michael and Fiona get information from a local drug dealer and are able locate Harrick, who is holding Sam in a barge on the Miami River. In the meantime, Michael has to convince the government agents that are pursuing him that he will cooperate if they give him time to rescue his friend.

Michael is able to kill Harrick and escape with Sam. With Sam now safe, Michael must give himself up to make good on his deal with the government agents. Following instructions found in Sam’s car Michael drives into a truck on a remote bridge with the promise that he will finally get some answers.

Since Michael is preoccupied with his burn notice, Sam decides to help Gillian Walsh, a supervisor at a defense contractor.  She is being blackmailed into using her security clearance to help smuggle Turkish heroin into the U.S.  Gillian’s friend, Melissa, is also being blackmailed but seems hesitant to help which Sam and Fiona soon discover why. Melissa and her husband Kent are involved in the heroin smuggling and have used Gillian to do the dirty work. Sam and Fiona turn to Michael for assistance in setting up a reverse-blackmail scheme.

Cornering Kent turns out to be a very dangerous and complicated proposition. Attempts on the lives of Michael and Gillian leave Sam and company no other option but to have Gillian smuggle one last batch of heroin and set Kent and Melissa up to get busted. A wrench is thrown into the plan when Kent’s employers show up to clean up loose ends. Kent and Melissa are murdered, Sam is kidnapped, and Fiona barely escapes.

Meanwhile, Michael is busy with his burn notice. The man who burned him, Phillip Cowan, has arrived in Miami and he wants talk to Michael in person. When their first meeting doesn’t happen, Michael and Cowan must trade coded messages to set up a secure meeting where all will be uncovered. When they finally meet, Cowan is shot and killed by a sniper, which leaves Michael wondering why he wasn’t the target.

Evelyn’s ex-husband, Doug, has abducted their son and gone into hiding.  As a result she has hired Michael to help find him.  Evelyn’s passion for protecting her son causes Michael to connect with her emotionally. This causes Fiona to get aggravated because of the way Michael is letting his emotions interfere with his judgment and she drops off the case. Michael gets a tip that Doug is hiding in the woods and finds out Evelyn is actually killer, hired to murder Doug before he can go into the witness protection program. Michael did all of the work to find her target; now she plans to finish the job.

Evelyn turns out to be a cunning opponent, as well as an admirer of Michael’s, and not the damsel in distress she was pretending to be. Evelyn is determined to finish the job and will stop at nothing to find Doug and kill him. She will not hesitate to go after the people Michael cares about to get the information she wants. Michael comes up with a plan to save Doug with assistance from Fiona and Sam.  Michael must think like an assassin and use the connection he had with Evelyn to get the best of her.

In the meantime, Michael’s plans to go to Washington D.C. to face the man who burned him are postponed when he finds out the man is coming to Miami to meet him instead.

Nick, a house sitter, is living very well on his client’s wealth, treating their property (sports cars, mansions) as if it were his own and bragging about it. Nick gets an unpleasant surprise when his fiancée, Dawn, is abducted.  Because the ransom is more than he could ever dream of paying he hires Michael to help him. Michael nabs Lucio, one of Daw’s kidnappers, and makes him a double agent, turning him against his own organization. With the help of Lucio, they set up the kidnappers with an opportunity too good to pass up. Posing as a disgruntled bodyguard looking to make easy cash Sam offers up Fiona, his “employer”.

They soon discover where Dawn is being held. While Michael creates a distraction, Fiona and Sam are able to stage Dawn’s rescue and reunite her with Nick. Dawn is not very pleased when she finds out Nick is a house sitter and not the wealthy person he pretended to be.

While all of this is going on, Michael is baffled by the arrival of a bureaucrat named Perry Clark.  Clark claims he may have a possible way out of Michael’s burn notice problems. Unfortunately the bureaucrat is not what he appears to be when he tries and nearly kills Michael.