Michael Scofield is imprisoned in Fox River State Penitentiary. He finds his brother, Lincoln Burrows, who is a death row prisoner, and tells him that he is going to break them both out of the prison.

Michael Scofield and Fernando Sucre (Amaury Nolasco) face a lockdown in order for the guards to search cells for contraband, where they're about to throw away a knife, but were stopped by Bellick (Wade Williams), who sends Sucre to SHU. Warden Pope (Stacy Keach) calls off the search for Michael's cell, but Bellick feels determined to, and sneaks into his cell when the prisoners are away, and finds the name "Allen Schweitzer". Bellick runs the name on the database, only to find no one matching it. Meanwhile, Sucre urges Stolte to let him call Maricruz (Camille Guaty), but is refused. Veronica (Robin Tunney) investigates who is framing Lincoln Burrows. She finds a tape, where she sees Lincoln shoot Terrence Steadman dead. Lincoln claims that he is being framed, stating the man was already dead and Lincoln never pulled the trigger. She attempts to talk to Crab Simmonds (Tab Baker), who didn't testify in his case, only to find out that he was killed of an apparent drug overdose. She is

Lincoln vows to make Abruzzi pay, but Scofield reminds him that Abruzzi is needed. Sucre is released from solitary and Scofield tests the former's loyalty before revealing his plan. Sucre passes the test, but he decides to change his cell and stay out of trouble as he will be released soon. Abruzzi realizes that he must befriend Scofield in order to find Fibonacci. Bagwell plans to lynch Scofield. Abruzzi tries to reconcile with Scofield by having his men beat up Bagwell and thus the latter going to the solitary. Scofield tells Abruzzi about his plan and he agrees to cooperate. L.J.'s probation officer forces him to visit Lincoln and the father and son become closer after a long time. Before Barris can sign her testimony for Lincoln written by Donovan, Kellerman and his fellow agent, Hale, abduct and kill the former. Donovan decides to leave her fiance, Sebastian Balfour. Bellick brings Patoshik, a psychotic inmate, to Scofield's cell. Patoshik becomes a problem for Scofield's plan.

Michael is three days behind on his plan to free his brother, particularly with his new insomniac cell mate, Haywire (Silas Weir Mitchell), whom he witnesses take some tablets to stay lucid, but escape when the doctors leave, describing them as "invisible handcuffs". He then notices Michael's tattoo and sees the hidden "maze" in it. Meanwhile, Veronica Donovan (Robin Tunney) meets with Nick Savrinn (Frank Grillo) from "Project Justice", who wants to assist. They question Lincoln regarding the evidence, which he insists was planted. Sucre (Amaury Nolasco) is visited by his cousin, Hector Avila (Kurt Caceres), who tells him that Maricruz (Camille Guaty) is with him now. He eventually gets hold of Maricruz, and learns that Hector told her lies to get her not to come. With this new development, Sucre urges Michael to get him back into the cell. Michael manages to get hold of two chemicals and uses them to corrode a pipe underneath the infirmary as part of the escape plan. He returns

Michael Scofield tells the team in his escape plan, now consisting of Sucre (Amaury Nolasco), Lincoln (Dominic Purcell), and John Abruzzi (Peter Stormare), that they have to take out either English, Fitz or Percy, the three names on his forearm from the tattoo. Meanwhile, Secret Service Agent Kellerman (Paul Adelstein) and Hale pay a visit to Warden Pope regarding Scofield's transfer. Pope denies the request, where the agents proceed in blackmailing him concerning the affair he had from Toledo, and threaten to tell his wife about this. Pope tells the agents that his wife already knows about the affair, but the agents know he did not tell her the whole truth. She knows nothing of the son he had there. Michael returns to his cell to find Pope, who tells him that some higher power wants him transferred out of Fox River. Michael plans to take the advice from Charles Westmoreland and get a transfer block letter, telling Pope he has sinusitis, to keep him in at least a month yet. However, Ke

Since Scofield's transfer was cancelled, the woman in Montana tells Kellerman to take care of Burrows quickly. He has an informant call an inmate in Fox River to kill Lincoln. The only form of identification of the inmate is an elastic bracelet. Veronica (Robin Tunney) avoids Nick Savrinn, until she realises that he is trying to help her all along, when he hears that the anonymous phone call to arrest Lincoln came from Washington D.C. Meanwhile, Michael (Wentworth Miller) realizes that to complete a digging job inside the walls to some pipes, he needs to spend a good block of time there, which has been proving difficult as he has to keep coming back to his cell to make count. After explaining this to Sucre (Amaury Nolasco), he is told that the only time count doesn't take place is during a lockdown. Michael manages to disable the prison's air conditioning. T-Bag (Robert Knepper) returns from the infirmary, where he is given a new cell mate, Seth. Since the A/C is off, the inmates suffe

Turk misleads Lincoln, by sending him into a secluded area, where he attempts to kill him. However, after the two men struggle, Lincoln pushes Turk over the edge, where he soon dies. Back in Michael's and Sucre's cell, T-Bag is keeping an eye on CO Hudson, who knows of the escape plan. Abruzzi enters the hole and helps Sucre with breaking down the wall. Sucre, a devout Roman Catholic, struggles with drilling through a depiction of the devil. Also adding to the dilemma is the fact that gas pipes lie behind the wall, and that drilling in the wrong place may cause a fatal explosion. However, together they are eventually both able to drill strategically placed holes and manages to break it down to see the pipe on the other side. Sara is still trapped in the room, where the rioters almost break through, and try to set fire to it, where Michael manages to arrive through the vents and rescues her from them. However, the rioters follow her and Michael, who try to evade them. Sara asks how M

Michael finds out a storage room, fundamental to the escape because it is the only building directly over the pipes, has been converted into a break room for the guards, and the team must find a way to set it on fire so that Abruzzi can get them assigned to PI work there. They have to convince Westmoreland, who is a trustee (and thus has access to the break room freely), to help them burn it down. Michael approaches him with his cat (who ran away during the riots), but he refuses to help. Meanwhile, Bellick starts an investigation into Bob's death, and upon hearing rumors that he died outside of Westmoreland's cell, he goes to question him. Westmoreland doesn't say anything, afraid of being considered a "snitch". Bellick tells him that if he doesn't get an answer before he leaves the cell, their friendship is over. Westmoreland still doesn't cooperate, and Bellick pets Marilyn, saying "...nice cat." A while later, Westmoreland returns to his cell and finds Marilyn dead on his bunk,

Seth "Cherry" Hoffner approaches Michael for help but his request is cut short by T-Bag who interjects and subtly threatens Michael to stay out of his business. Fearing for his escape plan, Michael concedes. When Seth asks him for help the second time, Michael turns his back on him. The team continues to work on pounding the concrete floor in the storage room during PI. Sucre worries over how they are going to dispose of the concrete fragments. Michael tells them to hide the fragments one piece at a time. They take the pieces out, littering and hiding them all over the yard. After Michael walks off, C-Note picks up one of the concrete fragments half hidden in the yard. As Michael and Sucre walk back to their cells, Seth jumps off from the second tier and hangs himself. Michael looks horrified. Michael tells Lincoln of Seth's suicide and how he felt responsible for his death. Lincoln tells him that it's not his fault and that he had to keep the escape plan safe. Michael relays tha

After John Abruzzi loses his power to control the prison industries (PI) when Philly Falzone ceases to pay Captain Brad Bellick, Michael Scofield and the other escape team inmates watch helplessly as PI is taken over. Abruzzi tells Michael the only way out is to tell his gang he still has control - and that means giving up Otto Fibonacci to them. Michael doesn't want to give up an innocent man's life, but ultimately hatches a plan with Abruzzi. Abruzzi's mob gang visits him in prison, then demands to know how Michael figured out the location. Michael explains that he did his homework - before they go into witness protection, they are in the custody of a local sheriff. Only one was out of town during Fibonacci's custody, and he made a lot of calls to his wife, which Michael intercepted. Pb fibonacci Fibonacci Abruzzi's Mobsters goes after Fibonacci, who they believe is in Canada. However, the RCMP cracks them before the assault. Fibonacci picks up a copy of a Kansas newspaper

Michael gets a visit from his wife, while Veronica and Nick get a visit from Quinn.

C-Note overhears Michael and Lincoln discussing that there are too many fugitives for available time and they share the information with the group telling that one shall be left behind. T-Bag feels threatened and calls his cousin James Bagwell, disclosing the escape plan and asking James to call the Warden Pope in case T-Bag does not contact him later. Abruzzi asks his outside man to kidnap James, but things go wrong and the mobster kills James and his five years old son Jimmy. Abruzzi feels guilty for the death of the child and feels the need of God's forgiveness, but T-Bag betrays Abruzzi like Judas. Meanwhile Veronica and LJ bring Nick to the hospital and while in surgery, LJ escapes to see the funeral of his mother. Daniel Hale sees the teenager in the cemetery but he does not arrest him; later he tells his wife that they should move to West and gives an anonymous call to Veronica scheduling a meeting in the Highland Cafe. Maricruz tells Sucre that she is pregnant but she will marr

The escape is about to go through when the team hits a stainless steel snag, while Veronica is just a moment too late to get all the information she needs to prove Lincoln's innocence.

With the pipe to the infirmary replaced and Lincoln's life hanging in the balance, Michael must rethink his plan to escape and save his brother's life. A fellow inmate may hold the key to preventing Lincoln's execution.

Michael's plan to escape has failed. While Lincoln is strapped to the electric chair, he sees an oddly familiar face in the crowd. Is there one last hope to save Lincoln's life, or has his journey reached an end?

Flashbacks provide exposition on how the inmates arrived at Fox River Penitentiary from The Company's framing of Lincoln to the creation of Michael's plan to save his brother's life.

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.

After the crash, Kellerman tries to suffocate Lincoln, but he is saved in the last moment by a stranger. Sucre leaves the solitary confinement and Michael tells to his partners that he has completed the map, but he needs the key of the infirmary. Abruzzi is back to Fox River, apparently converted in a religious man. Warden Pope sends Captain Bellick to find Lincoln before notifying the authorities. Nick tries to convince Veronica that they are losing time checking the calls of Quinn's cell phone. Michael kisses Sara and asks her to wait for him. Tweener is in trouble with Avocado and he castrates the abuser. Lincoln sees that the stranger is actually his father, and he explains that he worked for the powerful Company, and Lincoln is a victim of a big plot against him. He had leaked information of EcoField and they used Lincoln to force him to show off. Michaels asks for help to Nika. Veronica finds many calls from Montana. The Vice-President tells her brother that he is alive just beca

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 connection to a Fox River inmate.

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.