The fourth and final season of the serial drama television series Prison Break commenced airing in the United States on September 1, 2008. It consists of 24 episodes, 16 of which aired from September to December 2008. After a hiatus, it resumed on April 17, 2009 and concluded on May 15, 2009 with a two episode finale.
Michael is in Los Angeles to kill Gretchen and Whistler, while Linc, Sofia and LJ chill in Panama. SONA is burned down and Bellick, Sucre and T-bag escape.
After The Company attempts to kill all the main players, they re-unite under a new 'handler', Self (a Homeland Security agent), they go after the Company to attempt to bring down the shadow organization once and for all.
The Company continues to work on locating Michael, Linc and the team, while the brothers lead their team on a first assault to copy the Scylla data card.
Michael attempts to track the cardholder and avoid going back to prison. Wyatt finds new information regarding Sara's whereabouts. T-Bag uses a new identity to make a new life for himself.
With a camera phone far off, the gang gets an image of a license plate which is traced to a Turkish consulate Erol Tabak. As they are staking the man, Roland's data tracking device reveals that the cardholder is not the consul. It's his wife, Lisa Tabak.
Sara realizes that she's being followed and ditches her pursuer. Mahone meets up with his ex-wife to get the positive ID on their son's killer. Michael and Linc lead Bellick and Sucre on a dual mission to both find T-bag and break-in to the office of another cardholder (who happens to be a big-wig at Treasury with his office in the Federal Building).
The crew executes a daring attempt at the data on that card in the Federal Building, while T-bag continues to muddle along trying to figure out what he's landed himself into.
Mahone, meanwhile, has begun an odyssey to track and eliminate his son's killer that the team has also figured out is the assassin that is after them all.
Bellick causes a disturbance at a betting window of a racetrack to distract security. This allows Michael and Mahone to sneak into the operations manager's office and tape the device to the man's desk. Roland picks up the signal. Cardholder four is Nathaneal Edison, who has bet on a horse named SparkleKid. Lincoln does something to cause SparkleKid to get a late start from the gate. Edison is furious and goes to speak to the operations manager. With the card near the desk, Roland pulls all of the information off Edison's device.
Gretchen holds T-Bag hostage in his house and she cuts his arm with a knife. He reveals what little he knows about Scylla.
Flashback to 2001, Chicago: Lincoln and his old partner Derrick storm a limo and steal a briefcase of money from the guy inside. Present Day: Linc pitches the idea of raiding the General's limo.
Lincoln beats up Wyatt, demanding that he tell the General that they are dead. Wyatt doesn't give in. Michael and Sara convince Lincoln that this won't work. Agent Self brings a briefcase to the warehouse, and Sara warns Wyatt that he can save himself from what might be in the briefcase if he does what they ask. Self and the guys go over the blueprints but Gretchen has the remaining Bird Book pages to complete the document.
Michael’s (Wentworth Miller) medical condition takes a turn for the worse; Sucre (Amaury Nolasco) gets himself into an explosive situation; Mahone has designs on the Company’s architect; and Agent Self (Michael Rapaport) gains a surprising ally.
Michael and the gang make the final preparations for the break-in to steal Scylla; Gretchen (Jodi Lyn O’Keefe) uses her feminine wiles to get the final card key from the General (guest star Leon Russom); and T-Bag reaches the point of no return.
The search for Scylla has a shocking end as Michael comes face-to-face with the General and is betrayed by one of his own.
Agent Self hides Trishanne's body. He calls Stanton to explain that Michael and Lincoln ambushed him and killed Trishanne. Self then threatens T-Bag to get him to find Gretchen.
The team realizes that they have been double-crossed by Self. Michael calls Homeland Security looking for Self's superior. Mahone knows that Self must have played it this way to keep himself insulated. He thinks they should leave the warehouse. Michael hides a nosebleed.
Sara injects Michael. Meanwhile, at an abandoned building nearby, Lincoln sees Self's car pull up to the warehouse. Michael calls Self, who wants the missing piece. Self fires gas canisters at the team. Lincoln gets the drop on Self. Gretchen shows up with a drawn gun. She saves Self and the two escape.
Mahone meets with Lang and asks who he can trust.
The General tells Lincoln and Sara that they are guests in his home while Michael is undergoing surgery. Sara watches from the operating room observation. Michael dreams that he has woken up in his old prison cell. He talks to Charles Westmoreland and apologizes. Michael sees a blueprint of his mind. In the operating room, Michael is reciting the alphabet. Westmoreland tells Michael that he has the answers.
Lincoln pulls out some of T-Bag's teeth to get him to talk. Then Lincoln and Sucre leave the Company headquarters to go find Scylla.
Lincoln comes to Miami to recover Scylla, while Michael learns some surprising info from his past.
Michael and Sara journey to Miami while Lincoln meets with his mother. T-Bag and Self's mission to locate Scylla takes a dramatic turn. The General comes under pressure.
Michael and Lincoln come to blows over Scylla as Christina sets the wheels in motion for her plan. Meanwhile, Sara recieves life-changing news. T-Bag arrives at the Indian Embassy. The General becomes increasingly paranoid.
Michael calls Lincoln and tells him that Sandinsky's been working with Christina. He then calls Christina and asks about Sandinsky. She won't talk about him and asks to meet.
Michael and Lincoln, trapped in the hotel, make a run for it once spotted by the local police, led by Captain Hutchinson. They are trapped in the kitchen area. Michael calls Mahone and says that Scylla's gone; they need help getting out.
Michael insists to Mahone that he's going to find a way to save both Lincoln and Sara.
Michael and Sara talk about the ordinary life they're going to lead when this is all over.