"Chicago" is the thirty-eighth episode of the American television series 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.

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 regard to the casting for this particular episode, regular cast member Amaury Nolasco (who plays Sucre) does not appear.

At an Evansville, Indiana train station, Sara Tancredi (Sarah Wayne Callies) reunites with Michael Scofield (Wentworth Miller) and the two embrace. Sara also greets Michael's 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. 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. Lincoln and Michael stop her and save Kellerman.

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 justice for her father and her feelings for Michael. They kiss but are interrupted by a police rail block.

After running through the police rail block, 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.