A train pulls up in Evansville, Indiana and Sara steps off cautiously, looking around, and looks lost for a moment, but then catches sight of Michael waiting for her. Kellerman is hiding around the corner and gets another call from the President who is still trying to find out where he is. Kellerman starts off acting cold towards the President but he seems to be softening. Meanwhile, Sara reaches Michael who envelops her in a hug and holds her, knowing that she has been through a lot. Sara shows Michael the key, but he doesn’t know what it’s for, and he tells her about Kellerman working with them.
T-Bag wakes up next to Susan and starts kissing and embracing her and Susan doesn’t seem to be appreciating it. T-Bag tells her that he’ll get the kids and Susan tries to tell him no, but of course T-Bag doesn’t take no for an answer. He pulls off the pillow and reveals that Susan has been tied to the bed and cuts the rope. Susan attempts to tell T-Bag that this won’t work and that he needs to go, and then tells him that there will be someone visiting today. Even this doesn’t faze T-Bag.
Sara, Michael and Lincoln round the corner to where Kellerman is standing and Kellerman decides to speak first and tell Sara that it’s all behind them when Michael suddenly grabs him and pushes him against the wall. Michael reluctantly lets go because he knows that he needs Kellerman. Sara tries to convince Michael that they don’t need Kellerman and Kellerman tries to redeem himself by telling them immediately what the key is for. A private Cigar Club in Chicago.
Haywire is in tears and is hurriedly trying to sort out his raft so that he can float away because he knows that he has done a bad thing.
Mahone tells everyone to have Michael and Lincoln’s photos in every gas station because he thinks that they are still traveling by car. Wheeler comes and interrupts him and tells Mahone about Haywire’s recent murder. Even this doesn’t pull in Mahone as he tells Wheeler to send some agents to Wisconsin, but Wheeler reveals that Mahone isn’t in charge anymore. All his plans will go through Headquarters from now on. Mahone is annoyed, to say the least. Kim then picks the perfect time to call him and tell him that he wants Haywire eliminated. Mahone protests saying that he doesn’t know anything and that Haywire is mentally unstable but Kim isn’t taking any chances.
To get on the train to Chicago, Kellerman pretends that he is still part of the Secret Service and is transporting Michael to a prison and demands a carriage of his own. Linc and Sara are waiting for Kellerman’s signal outside and Linc reassures Sara and tries to comfort her but it doesn’t seem to work. Sara is understandably tense. When the coast is clear Kellerman signals to them and they climb aboard. Sara takes a seat opposite Michael and Kellerman and Linc spread out. You can cut through the tension with a knife.
Mahone goes to visit Bellick and Bellick isn’t too pleased that Mahone didn’t hold up his end of the bargain. But Mahone has come to surprise Bellick with a better deal. Freedom. In exchange, Mahone wants Bellick to find the escapees for him.
T-Bag is playing man of the house when Patty, Susan’s visitor comes over and Patty finds him charming as T-Bag feeds her a pack of lies. Zack is desperate and tells Patty to come see his new bike in the garage but T-Bag can see right through him and forces Zack back to the table.
Kellerman and Lincoln are sleeping while Sara is busy staring into the distance and replays her history with Kellerman/Lance and the memories are haunting her. Sara asks Michael to get her some water, and checks to make sure that Lincoln is sleeping and walks past Kellerman as he says to her “it’s never personal Sara”. Sara spins around starts to strangle Kellerman with a cord. Images of him torturing her go through her mind as she pulls harder. Lincoln and Michael come running and separate them reminding Sara that they need Kellerman. Kellerman isn’t too pleased with Sara and says that that was the first and only time that she would get away with something like that. The train conductor asks if there was a fight and Kellerman plays it down.
Bellick is now a freeman and Mahone’s dog. He finds a new car, gun, money and info about the escapees waiting for him and is on his way.
T-Bag is walking Patty to the door and continues the charm act as she flirts with him on her way out. T-Bag then decides that they need to leave and orders that the family go pack their bags.
In Minnesota C-Note tries to get an ailing Dede to eat something but she is too ill. A junkie comes in and waves a gun around and tries to rob the café but C-Note will have none of that.
Michael goes to the bathroom where Sara is and knocks on the door but Sara just wants to be alone for now. Michael goes back up and glares at Kellerman then sits with Linc who asks about what they’ll do after they open the box. Kellerman walks out of the carriage for some privacy and talks to the President again and tells her of his whereabouts, thinking that it will get him back into her inner circle.
C-Note is still very calm and helps the situation by being on everyone’s side, including the junkie thief.
Michael goes back to see how Sara is doing and she lets him in. Sara tells him of how she was thinking of what she had become, then professes her love to Michael, prompting him to kiss her. Their embrace is interrupted when the train starts to come to a screeching halt. They look out to find a roadblock. Lincoln climbs out of the train and dangerously crosses the train from the top and climbs into the drivers cabin and lets Michael, Kellerman and Sara in. Lincoln forces the driver to run the roadblock and the train smashes through the cars.
Bellick is sitting in his truck practicing his introduction until he gets it right. He then walks into Sascha’s house, who conveniently completely ignores his choice of introduction. Sascha doesn’t want to hear what Bellick has to say, but she has to when he threatens her into telling him about Haywire’s whereabouts. Bellick calls Mahone about Haywire and Mahone instructs Bellick to keep him there alone until Mahone gets there.
Lincoln, Michael, Kellerman and Sara are debating whether to jump because they know that there will be cops waiting for them in the next station.
C-Note negotiates with the junkie when the junkie tells everyone to wait in the storage room until the police come and C-Note tells him that he is a wanted man, so the junkie allows C-Note and Dede to leave but then grabs the waitress with the intention of raping her. C-Note debates running away or saving the waitress and decides on the latter. He knocks down the junkie but the police are here already. The police walk in but the grateful waitress has already lead C-Note out from the back.
Haywire is at his shelter with Larry his dog when Bellick finds him and Haywire runs.
The conductor tells the driver that the people who smashed through the roadblock are jumping off the train. The four are running for their lives with the police right behind them. However, as the police catch them we find out that it isn’t Michael, Kellerman, Lincoln and Sara, but three passengers and the conductor dressed up in their jackets. Michael, Lincoln, Kellerman and Sara make it to the station undetected. It turns out that Lincoln forced the conductor to give the driver false information then to jump off with the three passengers and to keep running.
Haywire is still running and climbs up a crane elevator to get away from Bellick. Mahone tells Bellick to keep him there.
While everyone else is looking for an unlocked car, Kellerman gets another call from the president. This time Kellerman is very suspicious and decides on a surprise question and asks the “President” where they celebrated his 35th birthday. It is then clear to Kellerman that it wasn’t Caroline at all, but Kim trying to trick him. A wrong move for Kim.
Mahone reaches the location and climbs up to be with Haywire but is too tense and halfway has to pop in a couple of his magic pills. Mahone continues going up the crane elevator and has a heart to heart with Haywire, and seems to develop a father son bond with him in that short time. Mahone comforts Haywire and tells him that it’s okay to jump and end everything instead of going back to prison.
Meanwhile back in Chicago, Michael, Sara, Lincoln and Kellerman are parked outside of the cigar club and Michael and Sara go in to find out what’s inside the box. On their way in, Michael stops Sara and says “me too”, in response to when she had professed her love for him earlier that day.
At the same time Mahone is still talking to haywire and who then decides to jump, but looks to Mahone for permission first. Mahone tells him that it’s okay and Haywire jumps. Mahone turns away and seems genuinely upset over what just happened and Bellick looks shocked.