In the last season, Michael, who seeks for vengeance of Sara's death, knows that Sara is still alive because the head in the box is belonged to someone else. Also, Michael knows that Whistler secretly works for the Company with Mahone. At that same time, Sucre and Bellick manage to escape from Sona. Don Self, a Homeland Security agent, teams up with Michael, Lincoln, Sucre, Mahone and Bellick. He wants them to take down the Company in exchange for their freedoms. After escaping from Gretchen Morgan, Sara assembles wth Michael. They try to steal data called "Scylla" from the Company because this data can take down the Company. Meanwhile, Wyatt, a covert agent from the Company, is pursuing them all. When they have Scylla, Don Self turns to be a double agent and plans to sell Scylla, but there is something happens before he can sell it. It turns out that Michael's mother is still alive, and she has Scylla.
At the half of the season, with episode named "SOB", Michael's mother named Christina tells Michael that Lincoln is not his biological brother. She also frames Michael and Lincoln for murdering the President of India's son to bring about politics war between China and India as she will gain advantage from both of them. In the episode called "Cowboys and Indians", Michael gets Scylla, but Lincoln is taken by Christina, and Sara is taken by General Krantz. Michael has to choose between Lincoln and Sara's life. Eventually, Michael can save both Lincoln and Sara. They can escape with the help of Paul Kellerman, a former agent. Kellerman takes Scylla to the UN. The Company is taken down, and it becomes clear that they all are guiltless except T-Bag. T-Bag is sent to imprison again at Fox River, and General Krantz is sentenced to death by electronic execution. The Finale is four years later. They gather to recall the day Michael is dead. There is a clue on Michael's deadth on a special episode called "The Final Break."
