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Chicago is the thirty-eighth episode of Prison Break and is the sixteenth episode of its second season. It was written by Nick Santora and Matt Olmstead, and directed by Jesse Bochco. The episode first aired on February 5, 2007, making it the first episode to be aired during the February sweeps in the United States. It attained an average of 10.1 million viewers, which is the highest recorded audience for the second season so far.
The premise of this episode covers Michael Scofield and Lincoln Burrows' journey to Chicago with Sara Tancredi and Paul Kellerman. Other subplots include that of Agent Mahone, Bellick, T-Bag, C-Note and Haywire. In regards to the casting for this particular episode, regular cast member Amaury Nolasco (who plays Sucre) does not appear.
At an Evansville train station, Sara meets Michael and his brother, Lincoln Burrows (Dominic Purcell) but also finds Paul Kellerman (Paul Adelstein) with them as he secretly converses with President Caroline Reynolds (Patricia Wettig) by mobile phone from around a corner. Michael strangles Kellerman while Lincoln holds him down, after finding out that Kellerman had tried to kill Sara. When they let go of him, Kellerman tells the group that he recognizes Sara's key as being from a private cigar club in Chicago, Illinois.
Kellerman successfully deceives the train conductor by explaining that Michael is a fugitive, and he needs an empty train to transport him to Chicago. In the meantime, Lincoln thanks Sara for helping them and assures her that Kellerman is a temporary ally. On the train, Sara is struggling with flashbacks of her ordeal with Kellerman. As she passes, Kellerman tells her, "It was never personal, Sara. War never is." After noticing that Lincoln was asleep, Sara sends Michael away on a fool's errand to get water for her. Once he leaves, she gets behind Kellerman and attempts to strangle him with a cord from her sweatshirt; a makeshift garrote. As the brothers break up the fight, Sara says to Kellerman, "Nothing personal."
Wanting to be alone, Sara stays in the train car restroom. Kellerman calls the President, who promises him a job as "Chief of Staff". Michael enters the bathroom and talks to Sara. She asks him if he really believes they can "get it all back" and he replies that he has faith, and that it's kept him going the whole time. Sara says that she's motivated by revenge for her father and her feelings for Michael, and Michael responds by kissing Sara. They make out passionately for awhile, but are interrupted by a police railblock.
After running through a police railblock, the group of four has apparently jumped off the train. A police force chases the group, until their path is blocked by a helicopter. The group turns out to be the conductor and others, who explained that the real group of fugitives told them to jump off the train at gunpoint, to keep running, and not to look back. As Michael, Lincoln, Sara, and Kellerman leave the train without incident, Kellerman finds a car, and is again contacted by the president. Kellerman asks her what they did during his 35th birthday. When the voice on the other line cannot answer the question, Kellerman realizes that she is not actually the President. He says, "Hey. Whoever this is ... tell Bill Kim that he just screwed up ... big-time."
In Chicago, Kellerman offers to go to the cigar club with the key as he is not a "wanted fugitive". Michael and Sara go together instead. As they enter the club, Michael admits his feelings for Sara.
In Ness City, Kansas, T-Bag (Robert Knepper) forces his hostages, Susan Hollander (K.K. Dodds) and her children, to pretend that they are a family. A neighbour, Patty, arrives at the Hollander household. When Susan's son, Zach, attempts to take Patty aside to explain that they're being held hostage, T-Bag silently threatens Zach with his gun. Wary of their neighbours, T-Bag forces the Hollander family to leave the house with him.
In Benson, Minnesota, C-Note (Rockmond Dunbar) is at a diner with his daughter, Dede, where she is unable to digest her food and vomits in the bathroom. As C-Note prepares to leave the diner, an armed robber enters and attempts to rob the customers. C-Note attempts to diffuse the situation by telling the hostages to stay in one corner and give the robber their money. After the diner robber acquires the money, he tries to take a young woman with him as the police approaches. C-Note saves the woman and in return for his good deed, the hostages help C-Note and Dede escape when the police arrived.
At the Federal Bureau of Investigation Chicago Field Office, Agent Wheeler (Jason Davis) reports to Agent Alexander Mahone (William Fichtner) that Haywire has killed a man in Wisconsin. When Mahone says to let the Madison, Wisconsin FBI office handle Haywire and to continue focusing on the brothers, Wheeler tells him that he will report back to the headquarters. Agent William Kim (Reggie Lee) phones Mahone and orders him to kill Haywire because he was Scofield's cellmate and there's no telling what he may know about the conspiracy.
Mahone returns to Fox River State Penitentiary where he tells Brad Bellick (Wade Williams) that since the prosecution violated his rights, the murder charge will be dropped upon a Habeas Corpus hearing. However, in order for that to happen, Mahone wants his help to track down the fugitives like a "junkyard dog". Bellick complies. After Bellick is released from prison, he is given a car, a file with his name on it, along with a firearm and a badge.
On an Algoma, Wisconsin shore, Haywire (Silas Weir Mitchell) tries to make his escape on his makeshift boat with his border collie. Bellick arrives in Algoma and interrogates Sasha. After finding out where Haywire is, Bellick reports to Mahone. Bellick heads to the location and as he closes in on him, Haywire climbs up a silo. Mahone climbs up the silo to meet Haywire. As they converse, Mahone gives Haywire some subtle prodding to make him think that there is only one way out. Haywire jumps to his death.
- The song that was used to link the scene where T-Bag leaves Ness City with the Hollanders.
- The scene with C-Note in the diner is "Give Me Just a Little More Time".
- Towards the end of the episode where Haywire falls to his death, the song playing is "Home" by Alexi Murdoch. Another Murdoch song, "Orange Sky", was played during the Prison Break episode "English, Fitz, or Percy".
- The episode was filmed in downtown Greenville, Texas and in areas near Greenville. Although the filming was scheduled to begin on December 13, 2005, it was delayed to December 15, 2005. The action sequence, which involved the train crashing into police cars, was also delayed to January 8, 2006 and was filmed in an area just north of Greenville.