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.

Fiona’s new job as a bounty hunter puts her in contact with Thomas McKee, an accused brooch thief. She hides him in her apartment believing he is innocent and contacts Michael to help her clear his name. Michael must first locate the jewelry and actual thief. After finding out the culprit is desperate hotel owner, Lawrence Henderson, Michael comes up with a plan to steal the brooch back. Michael determines a break in would be impossible after scoping out Lawrence’s home because of the tight security.  Michael decides to use psy-ops techniques in order to convince Lawrence that being robbed is not only possible, but likely.   In doing so he hopes Lawrence will move the brooch into the open, where he can be busted with the jewelry. While all of this is going on Fiona uses her time with Thomas to make Michael jealous, though the results may not be what she anticipated.

In the mean time Michael also needs to flush out the man who burned him, Philip Cowan. With the promise of providing information that would benefit Fiona’s Libyan connections, he is able to get the Libyans to frame Cowan. Michael’s plan is deemed successful when he gets a phone call from a livid Philip Cowan, the man who burned him.

Ernie Paseo’s business is being ruined by a group of local thugs who bully him and his customers. Michael agrees to help but quickly discovers that they are part of a much larger and more dangerous criminal organization run by, Concha Ramirez, a gorgeous but cold-blooded woman. Michael poses as an insane thief in an attempt to scare off the gang, and manages to give the thugs a taste of their own medicine. This activity impresses Concha so much that she recruits him to kill Ernie Paseo and his entire family. Michael befriends Concha’s right hand man, Diego, and convinces him that he’s going to be killed by his boss; because of this Michael is able to get the best of Concha.

During this job Michael is able to get the turn the tables on CSS Agent Bly, who is now bullying Sam and Fiona. Michael is able to blackmail Bly into giving him a copy of his burn notice by setting up off-shore bank accounts in Bly’s name.

Virgil, an ex-Navy Seal who once saved Sam’s life, is beaten when he tries to repossess a speed boat from a gang of Jamaicans. Virgil hires Michael to finish the job he started. When Michael attempts to return the boat to Virgil’s client, he finds that the client is a crooked cop and that there is ten million dollars hidden in the boat. Michael knows that both Jamaicans and crooked cops will come looking for Virgil so he hides him at his mom’s house, never imaging a romance could be sparked between the two. Not surprisingly both the Jamaicans and the cops want the money. Posing as Homer, one of Virgil’s devoted employees, Michael must negotiate a solution. Michael promises the money to both, and is able to keep them at bay long enough to devise a plan. The plan is quickly abandoned when Virgil is kidnapped while by the Jamaicans while out on a date with Madeline. All of this leads to a deserted bridge where the money is set on fire and shootout ensues between the cops and Jamaicans. Michael is able to escape with Virgil and some of the money with the assistance of both Fiona and Sam.

As if he wasn’t busy enough, Michael must also contend with a CSS agent who refuses to identify himself.  The agent tries to bully Michael into forgetting about his burn notice. Michael is able to outwit the agent his identity with the help of Fiona’s skill as a pick pocket.

Nate, Michael’s brother, introduces him to Jake Miller, a supervisor at an airport who has been accepting small gifts from a family of exporters in exchange for small favors. When offered a large gift for a highly illegal favor, Jake declined and then began receiving began. Michael quickly discovers these “exporters” are actually gun runners who trade in stolen military weaponry. The head of the family is a former Mossad officer who and not easily intimidated. Michael poses as an international arms dealer and befriends Eli’s black sheep son, Ari. He convinces Ari that he could impress his dad by doing a large deal with him. Through the friendship Michael is able to view the inner workings of the operation, disrupt it, and spook Eli and his family into leaving Miami.

In the meantime the FBI is starting to put more pressure on Sam to get something on Michael. Michael finds out about this and arranges for Sam to “steal” his burn notice and turn it in to them. This ploy gets the attention of people higher up the chain and a new group of intelligence officers are sent to Miami to investigate.

An assassin with a grudge against Michael arrives in Miami. In an attempt to obtain information on his burn notice, Michael tries to capture his would be killer. Meanwhile, a childhood friend of Michael’s, Bill, is in desperate need of assistance. Bill’s eighteen year old daughter has been lured into a prostitution ring under the promise of a modeling career. Posing as a client, Michael meets the man in charge of the ring, Carl Wilhelm, and finds out Jenna is scheduled to leave the country in a few days. With the help of Sam, Fiona and his brother Nate, Michael attempts to rescue Jenna. When that doesn’t work, he kidnaps Carl’s brother, Oscar, and uses him as leverage to get Jenna back to her father.

Michael’s landlord, Oleg, reaches out to him to help his best waitress Cara. She stopped coming to work after receiving death threats. Michael sees it as an opportunity to live rent-free for the next few months, that is until he finds out that a Colombian cartel is behind the threats. Cara was the only one to see a brutal beating, and was able to visually identify the attacker, Alvaro DeSantos, for police. She’s been getting “anonymous” threats against her life ever since and the cops are not providing protection. Michael first tries to help Cara get out of Miami but this is made difficult by her seventeen year old daughter’s reluctance to leave her life behind. In order to keep the mother and daughter safe in Miami, Michael must turn the cartel against DeSantos. In the meantime Michael is able to make contact with an old spy friend of his who is in Miami to attend a conference under diplomatic cover. This man is his means to getting confidential information about his burn notice and Michael isn’t above using a little blackmail to get it. Finally, Michael saves the lives of the desperate mother and daughter while obtaining his first tangible lead; the burn notice tracking number.