Sara, Michael, and Lincoln are reunited at a train station. Sara shows the brothers the key her father gave her. Around the corner Kellerman gets a call from the President. She tells him she's speaking in Chicago, and wants him to bring in the brothers. Michael tells Sara, "We've got someone working with us now." Sara looks up and sees Kellerman. T-Bag wakes up next to Susan who he's tied to the bed. She tries to convince him that sooner or later someone will notice she's not going to work, and the kids aren't in school. She brings up her friend Patty, who's coming over this afternoon. T-Bag says he'll take care of it. Michael chokes Kellerman while Lincoln holds a gun on him and wonders, "How long you can hold your breath?" Kellerman sputters that they need him. He spies Sara's key. He says he knows what it's for: a private cigar club in Chicago. Agent Kim orders Mahone to get after Haywire. He points out that Haywire was Michael's cellmate, and may have heard something that could help them.

Kellerman drags Michael to an approaching train conductor. He flashes his badge, and says he's Secret Service and is escorting a prisoner. He wants an entire car cleared out so he can escort the very dangerous criminal in peace. The conductor complies. Once he's gone, Kellerman waves Lincoln and Sara into the car. Mahone visits Bellick, who's mad that he's not been segregated from the other prisoners. Mahone offers to set aside Bellick's conviction if Bellick will "unofficially" work for him to bring in the escapees. Brad jumps at the chance to be set free. T-Bag's charms Susan's friend Patty over lunch while the family squirms. On the way to Chicago, Sara asks Michael for some water. He gets up to get it, and she follows. As soon as Michael is out of the car, Sara walks up behind Kellerman and wraps a cord around his neck to strangle him. Lincoln and Michael manage to stop her just in time. Kellerman warns her, "One of those, you get one of those. One!"

Bellick walks out of Fox River a free man. He has a car, a gun, and a badge. After T-Bag gets rid of Patty, he realizes this life isn't going to work. He then announces they're moving, and orders everyone to pack. C-Note and Dede are at a diner in Minnesota when in bursts a robber, high on something and brandishing a gun. Kellerman calls the President, and tells her he's on a train to Chicago. She offers him the position of Chief of Staff. The crazed robber punches a patron. Things get tense until C-Note takes charge and calms everyone down. He starts collecting everyone's valuables. Michael and Sara have a private moment. She confesses her feelings for him, and they kiss. Their kiss is interrupted by the screeching of the train's brakes. The police have set up a roadblock. Lincoln climbs on top of the train, makes his way to the engine, and at gunpoint orders the engineer to run the roadblock. Bellick talks to the girl whose dad Haywire killed, and gets a lead on him. He informs Mahone, and Mahone is on his way.

C-Note hands over everyone's valuables to the thief. The gunman says he's going to lock them in the back room, where they can wait for the cops to show up. C-Note tries to talk the man into letting him go. In front of everyone he explains that he's a wanted man. He says his daughter's sick, and he has to get away. The gunman agrees to let them go. He orders everyone else into the back room... except for a pretty waitress, who he wants for himself. C-Note can't abandon the girl, and punches out the punk. Moments later the cops arrive, and ask who disarmed the robber. The guy the robber punched earlier says he did. At that moment the grateful waitress shows C-Note and Dede out the back door. Bellick chases Haywire up a grain silo. Mahone arrives, and climbs up after him. Haywire pleads with Mahone not to take him back to prison. The train's engineer calls in that he's got some jumpers: one woman and three men. Three men and a woman jump from the speeding train, and the police chase them into the woods. They finally catch them, but it's the conductor and three other passengers. They were threatened that if they didn't run, they would be shot. Michael has turned the tables again: he forced the engineer to make a fake call. The train rolls on to Chicago. Mahone tells Haywire he doesn't have to go back to prison: there is a way out for him. As confused as Haywire is, he seems to finally understand this is the end of the line. Mahone sadly watches as Haywire calmly leaps to his death.