Lincoln Burrows is currently on death row and scheduled to die in a few months for an assassination his younger brother, Michael, is convinced he did not commit.
Lincoln Burrows is on death row for the murder of the vice president's brother. He insists he's innocent and only his brother Michael Scofield believes him. As an engineer who helped design the prison where Lincoln is being held, Michael takes drastic measures to help his brother. He gets himself arrested and sent to the same prison so that with his knowledge of the building the two of them can escape together.
Trouble is inevitable in the prison, with a race riot imminent. Michael has problems retrieving a screw from the bleachers. Veronica receives a security tape that shows Lincoln shooting Terrence Steadman.
Time is running out, and Michael must enlist the help of his cellmate, Sucre, to help execute his elaborate escape plan. Once Sucre realizes what Michael is up to, however, he decides that he doesn't want any part of it and asks for a cell transfer. Michael's new cellmate, Haywire, is trouble like his name. Unable to continue with his plan, Michael fears the worst. Meanwhile, Veronica's suspicions are growing as she meets a woman who may be able to help stop Lincoln's execution.
Seeing isn't believing when Haywire develops a fascination with Michael's elaborate torso tattoo, which further delays Michael's timetable for escape. Sucre has a change of heart when an unexpected visitor informs him of Maricruz's affairs. Lincoln's nightmares about his execution intensify. Veronica goes on the defense for Lincoln as she teams with an advocacy lawyer who may be more than interested in justice.
Kellerman and Hale pay a visit to Warden Pope, whose past may not be as angelic as it appears; Michael learns he may be getting out of Fox River much sooner than he expected - without Lincoln; Veronica and Nick's investigation to prove Lincoln's innocence makes Veronica doubt whom she can really trust; Michael must raise the roof as another piece of his escape plan.
Michael turns up the heat to break through to the other side (of his cell wall). Unbeknownst to Lincoln, outside forces plan to move up his execution day. Veronica and Nick track a lead to Washington, DC. A full scale riot in the prison threatens the lives of inmates and employees alike and gives T-Bag an opportunity to uncover a startling secret.
As the full-scale riot escalates, Michael faces a difficult decision regarding the life of Dr. Sara; Abruzzi and Sucre team up to break the devil's back; T-Bag tastes blood in his quest to be included in the escape plan; Lincoln has a potentially fatal confrontation; and Veronica and Nick track a lead to Washington, DC.
Michael's plan hits a snag when he discovers an old storage shed crucial to the escape has been turned into the guard's break room. Veronica and Nick get an explosive warning to back off their investigation to prove Lincoln's innocence; LJ goes on the run; the conspiracy claims three more lives; the identity of the mystery woman calling the shots is revealed.
Drops of blood bead along a newly inked line on Michael Scofield’s forearm. Sid, Michael’s tattoo artist, puts the finishing touches on a set of fanned playing cards. The suits of some of the cards remain hidden, but the numbers are visible on all ten.
Abruzzi struggles to get his crew back to PI. He tries to convince Michael to reveal Fibonacci's whereabouts to Falzone.
Agents Kellerman and Hale receive some professional help for their search, as the Vice President isn't satisfied about their progress so far.
An inmate becomes suspicious of the escapees' work in the break room.
Steadman's money trail leads Veronica and Nick to a surprising discovery.
Michael, five years younger, adjusts his tie in a streamlined office of an architecture firm overlooking the Chicago cityscape. The interviewer across the desk comments on Michael’s impressive resumé, then asks why Michael is interested in architecture. Michael speaks with a quiet passion about structure, design and function. The interviewer appears impressed in the young engineer in Michael and asks, “What about the future? Where do you see yourself in five years?”
After learning all the escapees can't make it over the prison wall, the group decides to get rid of T-Bag. T-Bag has a plan of his own that doesn't involve him staying inside. His "insurance", however, is too obvious for Abruzzi, who takes action to undermine it. Sucre gets some news from Maricruz.
The slow and labored thumping of a heartbeat pulses. Abruzzi strains to remain conscious as Sara pushes him across the yard in a stretcher. Sara presses a towel against the wound in his neck to help stem the flow of blood, meanwhile urging him to stay with her and keep breathing. A medical helicopter roars over the prison yard and sets down to meet the gurney on the lawn. Michael, C-Note, Westmoreland and Sucre sprint to the fence in their P.I. jumpsuits and watch in shock as Abruzzi is loaded onto the helicopter.
Michael and the other prisoners attempt to return to their cells without being detected. A C.O. becomes suspicious about a broken pipe.
At the same time, Veronica and Nick request a judge to postpone Lincoln's execution. Sara requests her dad, the governor, to review Lincoln's case. Michael tries to put a stay in the execution by fiddling with the chair's wirings.
As Lincoln is about to be executed, he sees his father in the viewing room. A phone call from Judge Kessler delays the execution. After reviewing the newly surfaced evidence, the judge orders the exhumation of Steadman's body.
Michael creates a new, more dangerous, break-out plan, involving going through the prison yard. An accident puts Michael's new plan in danger.
Flashbacks shed light on the past actions that led to the incarceration of Lincoln, Sucre, T-Bag and C-Note. The basis of Michael's ingenious break-out plan is revealed. Dr. Tancredi recalls how she ended up in Fox River State Penitentiary.
Lincoln is worried about Michael's sanity while Michael has trouble remembering some parts of the prison schematics. Sucre has to conceal the hole in the guard's break room. Warden Pope transfers Michael to solitary after he declines his request.
In an effort to recreate the missing piece of the tattoo, Michael gets transferred to the psych ward, seeking the help of Haywire. T-Bag and C-Note have to join forces.
Michael must get the key to the infirmary and enlist the help of an old face, while Lincoln learns the identity of his kidnapper and another inmate learns of the escape.
Westmoreland wants Michael to speed up the planned escape, and Bellick gets one step closer to unraveling it. Michael has to decide whether to involve Sara in the breakout plan. Tweener's devotion is put to a test. Veronica finds out that her ally has a connection to an inmate serving time at Fox River.
Everyone's ready to make their escapes across the high wire. Veronica and Nick realize they may be in over their heads. Agent Kellerman helps Vice President Reynolds calm down before her debate.
As the escape is in progress, Warden Pope and Captain Bellick begin a search to detain the escapees. Michael and company struggle to reach the airfield as the police is hot on their heels. Veronica discovers a major piece of evidence that could prove Lincoln's innocence. The Vice President is worried about losing her authority.