Michael Scofield is a desperate man in a desperate situation. His brother, Lincoln Burrows, was convicted of a crime he didn't commit and put on Death Row. Michael holds up a bank to get himself incarcerated alongside his brother in Fox River State Penitentiary, then sets in motion a series of elaborate plans to break Lincoln out and prove his innocence. Once out of jail, their perils aren't over - the brothers must flee to escape recapture and battle an intricate political conspiracy that puts everyone's life at risk.
Michael and Lincoln head to Los Angeles with the intention of destroying The Company - but their priorities are altered after they make a shocking discovery.
Self forces Michael and his gang to search for the Scylla card - but the former inmates must also join forces with a computer hacker.
Mahone seeks revenge on Wyatt, who is attempting to get information on Sara's whereabouts. T-Bag adopts a new identity.
Michael, Lincoln and Sucre gatecrash a police benefit event to get the next key card, Sara falls back into an old habit and T-Bag runs into some familiar faces.
Michael's search for the next Company key card takes him to the Treasury Department. Meanwhile, Sucre and Bellick remain hot on T-Bag's heels.
Michael faces a difficult decision when Mahone is arrested while searching for the next card, and Gretchen confronts T-Bag.
Michael encounters Gretchen when T-Bag lures him, Bellick and Mahone into a trap, while the rest of the gang find the next card in Las Vegas.
A daring plan is devised to steal the final keycard from Pad Man, but the team is unaware of a traitor within the group.
The team makes a dangerous journey through a 30,000-gallon water main to reach the Scylla facility, T-Bag fends off an investigation, and Mahone exacts revenge against Wyatt.
Sara is forced to take Michael to a hospital as his condition deteriorates, while Sucre and Lincoln feel out of their depth when they are left in charge of the operation.
The team puts the plan to steal Scylla into action, but fears for Michael's health threaten to disrupt its success.
Michael and the team pull off the heist and finally lay their hands on Scylla. After tricking Pad Man to obtain the last keycard, the gang looks forward to the end of their mission.
Don sets up the gang and blackmails Gretchen into finding him a buyer for Scylla, but a problem arises when a segment of the code is found to be missing.
Gretchen and Self take possession of Scylla and receive details of a buyer, while the Company promises Lincoln that Michael's life can be saved in exchange for a favour.
Michael undergoes surgery, Lincoln and Sucre race against the clock to complete their mission and Scylla's game-changing secret is revealed.
Linc, Self, Gretchen and T-Bag travel to Florida in search of the elusive Scylla, while Michael learns shocking news about his mother.
Michael and Sarah discover first-hand the dangers of hitch-hiking as they head for Miami, and Christina tells Lincoln about her plan to take control of the Company.
Michael and Lincoln fight over Scylla, and Christina puts her plan into action. T-Bag causes a stir at the Indian Embassy, while the increasingly paranoid Pad Man causes a death.
Michael's reunion with Christina is soured when she drops a bombshell regarding Lincoln, and T-Bag grows determined to prove he is worthy of being a member of the Company.
Christina puts the final pieces of her plan together, while Michael makes a decision that has deadly consequences.
With Sara and Lincoln's lives hanging in the balance, Michael receives help from old friends as he plots to bring down the Company.
Michael and the gang continue with their efforts to bring about the downfall of the Company.
Michael and Sara finally marry, but their happiness is short-lived when she is arrested for the murder of Christina Scofield.
Michael is reunited with the rest of the gang as they try to break a vulnerable Sara out of prison.