Lincoln Burrows is scheduled to die on death row for an assassination his younger brother Michael is convinced he did not commit. With no other options and time running out, Michael takes drastic measures to get incarcerated alongside his brother. Once inside, Michael - a structural engineer with the blueprints for the prison - begins to execute an elaborate plan to break Lincoln out and prove ...

As racial tensions simmer inside the prison and Veronica digs into Lincoln's case, Michael tries to get a drug that will help him test positive for diabetes, and to secure a large bolt he can use in his escape plan.

Time is running out, and Michael must enlist the help of his cellmate Sucre to help execute his elaborate escape plan. But Sucre wants no part of it and asks for a cell transfer, and Michael's new cellmate Haywire is even worse than he sounds. Meanwhile, Veronica meets a woman who may be able to help stop Lincoln's execution.

When Haywire sees through Michael's plans, it further delays his timetable for an escape. Meanwhile, Sucre has a change of heart and Lincoln's nightmares about his execution intensify. Outside the walls, Veronica teams with an advocacy lawyer who may be driven by more than justice.

Kellerman and Hale pay a visit to Warden Pope, whose past may not be as angelic as it appears. Meanwhile, Michael learns he may be getting out of Fox River much sooner than he expected – without Lincoln. Outside the walls, Veronica and Nick's investigation to prove Lincoln's innocence gives her doubts of her own.

Michael turns up the heat to break through to the other side of his cell wall and outside forces plan to move up Lincoln’s execution day. Meanwhile, a full-scale riot in the prison threatens lives and gives T-Bag an opportunity to uncover a startling secret. Outside the walls, Veronica and Nick track a lead to Washington, DC.

As the full-scale riot escalates, Michael faces a difficult decision regarding the life of Dr. Sara, and Abruzzi and Sucre team up to break the devil’s back. Meanwhile, T-Bag tastes blood as his quest to be included in the escape plan continues and Lincoln has a potentially fatal confrontation.

Michael's plan hits a snag when he discovers an old storage shed crucial to the escape has been turned into a break room. Meanwhile, LJ goes on the lam and the conspiracy claims three more lives. And outside the walls, Veronica and Nick get an explosive warning to back off their investigation and the identity of a mystery woman calling the shots is finally revealed.

When Abruzzi is demoted in the prison hierarchy, the entire escape plan is put at risk. T-Bag's latest relationship sours so he targets someone new, and Michael is torn between wanting to protect the new kid and fearing T-Bag will reveal the escape plan to the guards. In the aftermath of the double murder, LJ runs for his life.

In order to get Abruzzi back in command of the prison's work detail -- and the escape plan back on track -- Michael must give up Fibonnaci's location to Philly Falzone. Meanwhile, Michael and Dr. Sara grow closer as the escape gang grows by one. Outside the walls, Kellerman and Hale get some unwanted help tracking down LJ, and Veronica and Nick make a breakthrough.

Dr. Sara and the escape gang are shocked to discover the identity of Michael's latest visitor, who brings him a priceless piece of the plan. Meanwhile, Captain Bellick becomes more suspicious and Tweener's pickpocketing skills buy Michael some valuable time. Outside the walls, Quinn lures Veronica, Nick and LJ to a cabin in the woods, while Kellerman and Hale have a life-threatening differen...

With proof that his escape plan is working, Michael must suit up to overcome the vertical limits of his last obstacle. As the escape attempt draws near, the group tries to reduce their number by one. Outside the prison walls, LJ slips away to attend his mother's funeral and Veronica gets a call from an unlikely source who sheds some light on the case.

With Lincoln's execution scheduled for the following day, Veronica reaches out to him and gains a newsworthy ally in the process. Meanwhile, Michael must find a way to get Lincoln out of solitary confinement and the inmates risk everything as they attempt the escape of their lives.

Michael tries, and fails, to delay Lincoln's execution by tampering with the electric chair as Lincoln's time runs out. Veronica and Nick pursue an exhumation order for Terence Steadman's body.

Lincoln, who thinks he sees his father at the execution, wins a two-week stay when a judge orders Terence Steadman's body exhumed. Sucre calls in a favor to help Michael verify a new route to the infirmary through the complicated drain system.

A series of flashbacks to three years ago unveils how Lincoln, Sucre, T-Bag, C-Note and Dr. Sara landed in Fox River State Penitentiary, and what drove Michael to craft his elaborate plan to break his condemned sibling out of the prison.

As Michael struggles to remember missing pieces of the prison schematics, Warden Pope places him in solitary when he refuses to name names. Meanwhile, Sucre is left to pave over the escape hole in the guards' room before a carpeting team can find it.

Transferred to the psych ward, Michael tries to clear Haywire's head and jog his memory of the missing piece of the blueprint tattoo; Bellick wants to auction off Michael's cell to the highest bidder; C-Note and T-Bag must team up in a high-stakes poker game, while Sucre's cousin Manche seems to hold all the cards.

The mystery man reveals himself to Lincoln as well as his connection to some bad company; when Michael realizes Sara holds the key to the escape plan, he takes their relationship to another level; Fox River turns into a mob scene when a familiar face returns; Tweener must choose sides; and Bellick may finally discover the "hole" truth on the “"he Key."

Westmoreland uses Bellick to plug a hole in the escape plan, which forces Michael to move up the breakout timetable. A fearful Tweener pledges his loyalty to Michael and in return may get out of jail for free; Michael feels that he has no choice but to involve Sara in the plan and must betray his father figure; and Veronica finds her life in jeopardy from her closest ally, who has a surprising ...

Dr. Sarah questions if she should leave a light on and the door open for Michael, who must betray the Pope in order to carry out his escape plan. Veronica finds evidence that points her to Montana, but realizes that her closest ally may actually be her greatest enemy. Michael, Lincoln and the other inmates make a break for it, but after the alarm is sounded, find out who will make it over the w...

With the escape in motion, Michael, Lincoln and the inmates take flight outside the prison walls, risking life and limb to evade capture. Warden Pope and Captain Bellick embark on a relentless pursuit to capture the escapees; the Vice President fears she will lose her command as well as her life; and Veronica tracks down the most significant piece of evidence to prove Lincoln's innocence.