Two steps forward and one step back. Michael gets Abruzzi on his side and proves Sucre's trustworthiness, but then loses a valuable piece of his plan.

Michael gets more of the tools and people he needs, but someone very high up has taken notice and started wondering what he's up to.

Having burned his shoulder, Michael's tattoo that showed the path through psych ward is now incomplete. With another inmate intimidated into snitching about the escape plans, Michael Scofield must use his wits to find a new way out of Fox River.

Improvising a new plan, Michael seeks out an acquaintance who may hold the key to his escape plan. In gen pop, the other members of the P.I. crew learn that the guards are auctioning Michael's cell to the highest bidder. Lincoln and Sucre devise a scheme to get Michael returned to gen pop. Veronica informs Lincoln that L.J will be tried for his mother's murder, and Lincoln desires to see his son.

The team start the escape from the hole in Scofield's cell.

As the escape continues, lives are lost and Pope and Bellick do everything in their power to capture the convicts.

With hospitals and clinics under surveillance, Michael brings Lincoln to Nika's home to heal his wounded leg. Then he returns to the place where he parked his Accord and finds that the car has been towed. Meanwhile agent Mahone retrieves Michael's backpack with his passport from a vagrant that broke the rear window of Michael's car to steal the backpack. Michael goes to Brewster Towing yard to recover his car. Meanwhile Sucre finds that Maricruz will marry Hector in a couple of days and he heads to New York in a stolen car. Sara is arrested and her father visits her, pays her bail and orders her to tell a fake version about the incident in Fox River since he will be the next Vice-President of United States. Later she goes to rehabilitation where Kellerman is pretending to be an addicted patient. C-Note schedules a meeting with his wife, but his conversation is bugged by agent Mahone. Bellick and Geary meet each other by chance and later they team-up to get the $400,000 reward for capturing Michael and Lincoln. They go to Fox River and Bellick interrogates Manche Sanchez, who discloses the plan of the fugitives. Michael and Lincoln forge a car accident to escape from Mahone, but they do not see that Bellick and Geary are in their tail.

Mahone arrives in Salt Lake City, trying to locate exactly where in Utah the escapees are. Michael and Linc hatch a plan with T-Bag and Tweener that will enable them to dig in the right place. C-Note and Sucre meet on the highway and head toward Tooele. Kellerman, in Washington, D.C., briefs Kim. Governor Tancredi phones Sara with a warning.

Michael's plan has hit a snag when the home owner's daughter, a cop, arrives. Mahone argues with Lyle Sands about how to proceed, but ultimately hopes that Tweener, in FBI custody, will reveal the location of the other escapees. Sara is now suspicious of Kellerman, so he tries something different to find Lincoln Burrows. In an Arizona detention facility, L.J. finds out he's to be released the next day; Linc drives to get him. Haywire, in Wisconsin, steals supplies from a camping shop.

The Border Patrol arrests Michael and Lincoln, saving them from Mahone that claims that wants his life back. Sucre crosses the border and jumps in a parachute in the Sonora Desert in Mexico. T-Bag goes to a war veteran bar in Pratt, Kansas, and steals a prosthetic job from a veteran sergeant. Michael and Lincoln are apprehended in the Border Patrol Holding Facility, in Las Cruces, New Mexico, waiting for transportation to Fox River, but Bill Kim orders Mahone to kill them. T-Bag meets Denise, who works in the post office, and seduces her to get Susan Hollander's address. Bellick is sent to the District Court in Greeley County, Kansas, and has his bail denied. He makes a deal to be sent to Fox River expecting to have a good life. However the new warden decides to use him as an example of the new administration. Meanwhile Mahone tries to transport the prisoners, but the standard procedure does not allow it. Kellerman makes an arrangement to intercept the convoy in a blocked tunnel to kill the prisoners. However, Michael and Lincoln and helped by a surprising allied. T-Bag finds Susan.

In Cutback, Montana, Kellerman lures the police and Michael and Lincoln abduct the cameraman Greg of Fox News and succeed in escaping from the siege. Michael and Lincoln decide to tape a message to be released in the Breaking News. Mahone is back in Chicago and analyzing the message; he interrogates Greg and he tells that he had overheard Michael tell that they should cover 460 miles in six hours. Mahone deduces that they intend to meet President Caroline in Denver. Wheeler discusses with Mahone and yells that the Internal Affairs department asked him to follow all moves of Mahone. Bellick is badly wounded in the infirmary of Fox River. Sucre befriends an old passenger in a bus to Ixtapa; however the driver asks him to leave the bus in a small town and Sucre robs the Volkswagen of the old man. In Algoma, Winsconsin, Haywire befriends a young couple and the girl has bruises on her arm; she tells that her abusive drunken father beat her.

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.

Aftermath of Sara's death, Lincoln decides not to tell about it to Michael. Susan B. told Lincoln that if he does something wrong again, she's going to send pieces from LJ to him. Meanwhile, Sucre got a job in Sona. And Sofia starts to help Linc.