Mahone calls Michael, and asks if he's made a decision. Michael doubts Mahone will let them go, considering his track record with the other escapees. Mahone reminds Michael he's a wanted man now; all he wants is to disappear. Michael agrees to the exchange. Michael says it'll take twenty-four hours to get there. A local boy approaches Michael, and offers him liquor or drugs. Michael sends him away. Lincoln tells Mahone he'll get the chair for what he's done. Mahone makes a call, and leaves a message for Kim. At Sara's trial Kellerman testifies in detail about Lincoln's set-up. The prosecutor asks what this has to do with Sara skipping bail. Kellerman says she had to run because he was under orders to kill her. Michael seeks out the drug-selling kid, Chaco. The charges against Sara are dropped because Kellerman brought documents to back up his testimony. He's then arrested. As he's led away he says: "It was nice knowing you, Sara." Kim calls Mahone, and is told to come down because he'll have both brothers there. Michael calls Sara, and leaves her a message.

As Sara leaves the courthouse she hears that the charges against Lincoln are being dropped. She tries to reach Michael to let him know, but can't... so she decides to go to him. Kim meets with his tightlipped boss. The man holds up notes with "SONA?" and "Just one is needed." The "one" refers to one of the brothers, and Kim knows which one. Under Lincoln's piercing glare, Mahone talks with Callie. He asks for another chance, and says they should go to Colombia since she always wanted to. She won't promise anything, but Mahone feels hopeful. Sucre leaves the hospital despite his nurse's objections. He calls the American embassy looking for Bellick. Bellick is pacing in a holding cell, and is happy when T-Bag is put in the cell with him. Chaco brings Michael to a yacht where his wealthy, drug-dealing boss is relaxing. The boss thinks Michael's a cop, and pulls a gun. Michael tells him to check the Internet for his name. They see Michael's picture, and a one-hundred-thousand dollar reward. Michael offers the man even more to help him. Lincoln works on his handcuffs as he tries to psych out Mahone. A guard takes Bellick from the holding cell, and escorts him to a police van. Sucre runs up as the van pulls away, pleading to know where Maricruz is. Bellick just screams that if Sucre wants to see her again, he'd better get him out of this. Sucre collapses in the street.

Michael makes it to Mahone's location, hides the bag of money, and enters the warehouse. Michael asks if Mahone is really going to let them go. Mahone informs the brothers that the Company doesn't want them dead, but alive. Kim calls, and Mahone gives their location. Then Mahone calls the police to report that a well-dressed Asian man has been shot by two Americans. Kim appears, and Mahone turns his gun on him. Kim came prepared for the double-cross: his own men storm in with guns drawn. Lincoln has unscrewed the pipe he is cuffed to, and breaks free. Guns blast away. The brothers and Mahone escape in the confusion. Michael grabs the bag of money, and Mahone takes off in the boat. Shackled and wearing an orange jumpsuit, Kellerman is loaded into a van. As they drive down the road the engine light comes on, and the van stops. One guard gets out to check it out. Kellerman tells the remaining guard: "In the French Resistance it was considered a high honor to face a firing squad. The highest honor was to smile when they shot you." The back doors open, and a masked gunman fires into the van. Mahone prepares to sail off on the Christina Rose when the police show up. They search the boat, and find two bags of cocaine that Michael planted. Mahone is arrested. Lincoln and Michael meet up with Chaco in the woods. He shows them a boat he bought with the money Michael gave him, and says she's very pretty. He's not talking about the boat: Michael is stunned to see Sara on board. She tells them Lincoln's been exonerated. Lincoln needs a drink, and Sara goes below to get one.

Kim shows up with his gun drawn. Lincoln tosses the money to Kim but he kicks it into the water, saying it's not about money. They're not done with the brothers yet, but only one of them will survive. He points the gun at Lincoln. A shot rings out, and Kim falls over... dead. Sara holds a smoking gun. The police run up, and the three run for it. Lincoln goes one way, and Sara and Michael go another. Sara and Michael are cornered in a shack. Sara breaks down over taking a life. Michael says they have to surrender, and takes the gun from her. He'll do everything he can to see she doesn't go to prison. They exit the shack, and Michael pretends to hold Sara hostage. Then he throws up his hands, and yells that he did it. Mahone calls Callie from jail, and heartbreakingly tells her to forget he ever existed. Lincoln makes it to the police station, and asks about Sara. A woman says she was released. Lincoln sees someone who might be Sara, but loses her in the crowd. A man visits T-Bag in jail. T-Bag screams that he did what they wanted. He got the brothers to Panama, and set them up. The man replies, "You got caught," and walks away. Michael and Mahone arrive at the federal prison. At the Basil Island Research Facility in New York, an underling gives the shadowy boss an update on Michael, and assumes Michael will try to escape. The old man says that is exactly what they want him to do. The season's final shot shows Michael stepping into the cold gray light of the prison... again.