Michael is in Los Angeles and prepared to enact revenge on the Company for killing Sara. He tracks Mahone, Gretchen and Whistler to a hotel where they are trying to retrieve a data card stolen from the Company. Whistler copied the card, unbeknownst to Gretchen. Michael traps them, and threatens to kill Gretchen until she lets him know that she faked Sara's death. They escape when the police arrive at the hotel.
Pad Man has Wyatt shoot Gretchen when he finds out that Whistler gave her a duplicate card.
Michael calls Lincoln in Panama City to tell him that Sara's still alive. Michael goes to the European Goldfinch site and sees a message from Mahone asking him to meet regarding Sara.
Mahone and Whistler are working together against the Company. Whistler has the data card that contains the names of the Company's agents. The card is referred to as Scylla. They need Michael to help them break into the Company, and they let him know that Sara might be in Chicago. Suddenly, Whistler is shot by Wyatt, who takes the Scylla card. Pad Man instructs Wyatt to get rid of all those who are close to Whistler.
Bellick and Sucre are rescued by Bellick's mother near the Mexico border. Meanwhile, in Panama City, T-Bag hires men to transport him over the border. He wants to go after Michael. T-Bag has the Bird Book and knows that it will lead him to Michael.
Mahone calls his ex-wife Pam in Colorado. She wants him to come home.
Lincoln is attacked on the street, but he manages to shoot the man in the chest. As the Panamanian police capture him, Sofia and LJ run.
Wyatt comes to Pam Mahone's house and forcibly enters.
Michael goes to Chicago to seek out Sara's family friend Bennett. The Chicago police arrest him and bring him to Homeland Agent Don Self, who wants Michael to help him get Scylla. Self had been working with Whistler. He offers to erase both his and Lincoln's sentences. Self is having Lincoln transported from Panama.
Mahone arrives at Pam's house where the police and paramedics have cordoned it off. Meanwhile, Sucre goes to the hospital to see Maricruz and the baby. The police are there and arrest him and Bellick.
Self explains to Michael and Lincoln that he wants them to be independent contractors to help him bring down the Company. Self will get them Mahone, Bellick and Sucre as accomplices. They will need to get the data card and then break into the Company's headquarters. This is the only way to de-encrypt what is on the card. They refuse to help Self.
Bennett brings Michael and Lincoln to see Sara. She has been in hiding. Yet Michael must help Self in order to wipe out his jail time. She is afraid they will never be safe, and she wants him to bring the Company down. The scars on her back convince Michael what he must do. A gunshot rings out in the safe house they are hiding in, and Lincoln, Michael and Sara escape. The Company has found them. They call Self to tell him they are in.
Lincoln and Michael meet up with Mahone, Bellick and Sucre at the Chicago police station. They know T-Bag has the Bird Book. Self gets the group fake IDs. Michael has his body tattoo removed.
Sara goes along with the guys on a cargo plane to follow Self and take down the Company.