Sara meets Michael and Lincoln in a train station in Evansville, Indiana; when she sees Kellerman with them, she becomes disturbed and upset. Kellerman tells that she has a key of a private cigar club in Chicago. Caroline calls Kellerman and he tells that he is heading to Chicago by train, and she promises his life back, inclusive the chief of staff position. T-Bag tells Susan that they are passing through an "adjustment period" in their lives; when she tells him that she will have a guest called Patty Wallace, T-Bag welcomes Patty with a magnificent family brunch and uses the strong father figure to discipline Zack, seducing the guest with his charm and attitude. Wheeler is reporting the actions of Mahone to the FBI Headquarter and they find that Haywire killed a man in Algoma, Wisconsin. Mahone visits Bellick in River Fox, releases him using a habeas-corpus to make his dirty work, and gives a car, a pistol and an FBI badge to the despicable man. Bellick chases and traps Haywire, and waits for Mahone. In Benson, Minnesota, C-Note and Dede are leaving a snack bar when an addicted thief announces a heist. When Kellerman sees a road block on the train, he realizes that he was betrayed.
- Michael arranges to meet Sarah at the train station where she sees Kellerman and recognizes him as the guy who tortured her for her father's key. Michael and Lincoln attack him, but Kellerman reminds them that he was there to help and that he knew the exact purpose of the key. It belonged to a vault in a cigar club in Chicago, so Kellerman convinces the train employee that he has to transport a fugitive to Chicago. The employee gives him a whole cart so Sarah and Lincoln go on the train. During the trip to Chicago on the train, Sarah has flashbacks of her times with Kellerman and the torturing, so she tells Michael to check if there is a bathroom on the carts. While Michael left and while Lincoln was sleeping, she grabs the string the key was hanging on and tries to suffocate Kellerman. Michael and Lincoln stop her in time. After catching his breath, Kellerman tries to attack Sarah, but Michael and Sarah hold them off. Sarah retreats to the bathroom, as the train employee tells Kellerman that a couple of passengers saw a fight going on inside their cart, Kellerman shakes that idea away. Michael goes to see if Sarah is ok in the bathroom, but she says she needs some time alone. Michael goes back again a while later and she lets him in. Sarah declares her love to him and the kiss. Then, the train shakes violently. Michael and Sarah leave the bathroom and find that there is a roadblock ahead. Lincoln climbs the train and crawls towards the front of it frightening the train conductor, but opens the door for Michael, Sarah and Kellerman to come in. They all threaten the conductor to go through the roadblock and to not stop. He does so, and they all decide that they have no other option but to jump. Mahone, in the meantime, visits Bellick and negotiates with him; Bellick helps Mahone in catching Haywire (who had killed a citizen) if Mahone helps Bellick. Meanwhile, Franklin eats with his daughter, DeDe in a diner. But DeDe doesn't feel good so they go to the bathroom as she gets sick. When they leave, they notice that the diner was getting robbed by a guy. He helps the guy to finish his business without hurting anyone. However the guy orders everyone to go to the storage room and to wait there until the police arrives. But Franklin tells him that he is a wanted man and the guy allows him to leave. But the guy, takes hold of the waitress and just as Franklin was about to help the waitress, the police arrives, so he quickly hits the robber until he was on the floor and the waitress helps him escape out of the backdoor. Meanwhile, Bellick corners Haywire who climbs a post and Mahone climbs after him. Haywire tells Mahone about Holland and how he wants to escape, while Mahone tells him that he knows exactly how he feels. So Haywire motions that he was going to jump and commit suicide and Mahone allows him freely to do so, and so he does. Meanwhile, at the train to Chicago, three guys and a girl jump from out of the train to escape the police. The police run after them and catch them. The four turn around and one shouts out: "please dont shoot, I'm a train employee". Michael, Lincoln, Sarah and Kellerman had ordered these people to jump for them and trick th cops. The train arrives in Chicago and Michael, Lincoln, Sarah and Kellerman all get out safe, just in time to escape the police who started searching the train. They all go to the cigar club. Kellerman, who was "supposedly" receiving phone calls from the president telling him to come back and bring the fugitives in, realizes that Bill Kim was behind the phone calls. Sarah and Michael enter the cigar club, and there Michael tells her: "me too." (As in, he loves her too).