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. With no other options and time winding down, Michael takes drastic measures to get himself incarcerated alongside his brother in Fox River State Penitentiary. Once he's inside, Michael, a structural engineer with the blueprints for the prison, begins to execute an elaborate plan to break Lincoln out and prove him innocent.
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 contacted by Leticia Barris (Adina Porter), Crab's girlfriend, but as they meet, she is spooked as Kellerman (Paul Adelstein) and Hale (Danny McCarthy) are watching.
Back in Fox River, Michael attempts to get to a bolt from a bleacher belonging to T-Bag (Robert Knepper), but is stopped. He doesn't want Scofield on the bleacher unless he will join in the racist battle between the whites and blacks, but he declines. On his second attempt, T-Bag's gang take the bolt off him, so eventually, he decides to join in to get at the bolt. However, C-Note (Rockmond Dunbar) sees this, and when he confronts Scofield regarding the PUGNAc, he refuses to give the pills. Soon, everyone comes out of their cell for count, when the riot starts. Michael decides to get the bolt back from T-Bag's cellmate (Brian Hamman), and does so after a struggle. C-Note sees this and stabs the cellmate several times; the wounded man dies in Michael's arms. T-Bag believes Michael killed the cellmate, and plans to get back at him. The fight stops through lockdown. Michael rubs the bolt until the end forms a hexagon shape key, big enough to unscrew the cell's toilet. It is explained that "Allen" is the screw, and "Schweitzer" is the lavatory.
After the lockdown is finished, C-Note decides to give him the PUGNAc due to his take in the riot, and tells him he will eventually find out what he's up to. Michael takes it, where Dr. Tancredi (Sarah Wayne Callies) gives him the test and finds out he is diabetic. Afterwards, Bellick takes Michael to an area, where Abruzzi (Peter Stormare) attempts to extract information regarding Fibonacci's whereabouts, but refuses to answer. Abruzzi has his men cut off two of Michael's toes to try to get him to talk.
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 to his cell and notices Haywire has drawn his entire tattoo and ponders the pathway. Michael purposely injures himself to get the officers to take Haywire away before the plan is exposed. Sucre gets transferred back to Michael's cell and continues the plan. Agent Kellerman (Paul Adelstein) suspects that Scofield may try to break Lincoln out and orders to transfer Scofield out the very next day.
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, Kellerman and Hale continue blackmailing him, and tells him to drop the paperwork, which he reluctantly does. Nick Savrinn and Veronica Donovan continue to try to find legal grounds to exonerate Lincoln. From the copy of the videotape of the murder, an expert believes that the gunshot sound was faked, but needs the original. However, they find it was destroyed in a "freak accident". When they return to Veronica's home, they find the copy has been stolen, and she suspects Nick may be involved.
Michael tells Abruzzi to get him a key to the warden's office. Abruzzi does this by melting toothbrushes into a stolen mold. Towards the end of the day, Michael, while constructing the model of the Taj Mahal, tells Pope that the structure will collapse if he does not remain there to hold the piece as the glue sets. Warden Pope leaves for the day and Michael immediately uses the replica key to leave the office through the back door and reach the roof. However, during count, Bellick realises a missing Scofield, and alerts the authorities. However, that was Michael's plan all along. English, Fitz and Percy are the names of the only three streets that lead to the prison and when the police cars come in response to the alarm, he learns that the cops only take English and Percy, leaving Fitz wide open. Now that he knows which path to take, he returns to the Warden's office, where he is found with the replica of the Taj Mahal. Nobody suspects anything. However, Pope says that Michael will be transferred, to Michael's dismay. The next morning, Michael is about to be transferred, but Pope decides to cancel it. Before Kellerman could get there, Pope admits to his wife the son he had during his affair. In another place, a mysterious woman tells the secret service to deal with Lincoln rather than Michael as he is Michael's weakness.
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 suffer in the heat, leading T-Bag to start a fight with Geary, who then initiates a lockdown while some of the prisoners are out of their cells. The prisoners riot and break into the prison cell control room, in which T-Bag opens all the cells and then finds a set of keys, giving him and the rioters access to the entire prison.
When news of the riot reaches the sick bay, the prisoners there also riot. After taking out the guard, they trap Dr. Tancredi (Sarah Wayne Callies) in the adjacent room. Michael uses a tracing of a devil from his tattoo to provide the coordinates (calculated using Hooke's law, also referred in this episode as hooker's law) needed to collapse part of the wall. This is vital to his escape plan as the wall prevents the team from entering a pipe that will take them to the infirmary. Meanwhile, after Lincoln is ambushed by T-Bag and his men, he holds new CO Bob Hudson hostage, who tries to escape, but T-Bag takes him to Michael's cell, where he learns of the escape plan, and blackmails Abruzzi (Peter Stormare) into getting in on the plan. Outside, the COs plan on stopping the riot, where Pope receives a call from Governor Tancredi, who is coming to Fox River.
Michael soon notices Dr. Tancredi's plight on CCTV and goes to rescue her through an air duct. Meanwhile, Charles Westmoreland stumbles upon a battered Lincoln and alerts him of the situation. A distraught Lincoln demands to know where Michael is. When Westmoreland is unable to answer, another prisoner named Turk steps forth to lead Lincoln to Michael, but it is revealed he is the inmate ordered to kill him.
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 Michael knows about the pipes and he replies by saying that he has had PI duties to clean up toxic mold in the pipes. Soon, Michael is able to knock out one of the leading inmates and rush to an exit. However, when they arrive, a sniper, sent by Govorner Tancredi, who is adamant to do what it takes to rescue his daughter, aims at him. Michael quickly ducks as the pursuing inmates are fired at and Sara reunites with her father.
Veronica and Nick arrive in Washington D. C. and receive the address from the placed phone call, a payphone. The payphone is next to the building of the company the Vice President uses. The phone rings and Veronica answers it. The caller tells them that they are dead. In a panic, Veronica and Nick run away from the payphone. Michael returns to gen-pop and reunites with Lincoln before heavily armed SORT teams invade the prison and force the inmates back to their cells. In Michael's cell, the team discuss what to do with Hudson. Michael, Lincoln and Sucre want to keep him alive. However, as he leaves, T-Bag kills him anyway, stabbing him in the stomach and throwing him down from the second level. Later, Sara asks a colleague why PI was ordered to clean up the toxic mold. The colleague replies that PI has never done such a job, which tells Sara that Michael's story was a lie. In the end, the prison is returned to normal and Michael can continue with his escape plan.
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, and spots Bellick looking down on his cell from the second level.
The next day, when Westmoreland goes to deliver the coffee to the break room, he looks at a pack of Bellick's cigarettes and his lighter. Meanwhile, while Michael and Lincoln do PI work, a fire erupts in the break room. Michael approaches Westmoreland and thanks him, but Westmoreland responds with "I didn't do it for you." The group begins by breaking through a drain in the floor and enlarging the hole so that they can fit through it.
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 that their mother taught them better, "When a man is down, you give them your hand." Meanwhile, a new inmate, David "Tweener" Apolskis tries to fit in. However, neither the black nor white inmates want to associate with him. T-Bag uses this opportunity to intimidate Tweener and suggests that he could be his new "friend". Tweener tells T-Bag to stay away from him. T-Bag is annoyed by his noncompliance.
Dr. Sara Tancredi inquires Michael's insurance company about the cost of his medical treatments at Fox River. She finds out that he had psychiatric insurance. Sara visits his psychiatrist who informs her of Michael's psychiatric condition. Michael has low latent inhibition and low self-worth. The psychiatrist tells her that Michael's condition coupled with his high I.Q., explains why he goes to such extraordinary lengths to help other people. After Sara learns this, she becomes more perplexed by who Michael is.
Michael notices Tweener's distress and decides to intervene. He hits T-Bag in the shin and warns him to stay away from Tweener. T-Bag again threatens him that he will tell the guards about the escape but Michael rebuts that he wants to escape just as much as the rest of them. T-Bag backs down. Later, when Tweener provokes him, T-Bag keeps on walking and eyes Michael angrily. Tweener, unaware of Michael's intervention, relaxes at T-Bag's retreat. Lincoln smiles at Michael proudly.
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.
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 in the meantime. Abruzzi confronts Michael, asking him how he feels. Both men are pleased with the results, but soon fall mysteriously ill.
During a scene in the C.O. break room, Michael, Lincoln, Abruzzi and Sucre reveals where they want to go after they have escaped. Abruzzi says Sardinia, Sucre says he wishes to get back to Maricruz, and Michael quietly says to Lincoln that together they will go to Darien Gap, Panama to live and perhaps run a scuba shop.
Meanwhile C-Note has noticed the disposition of cement from the break team. He offers the new head of P.I. $150 a month to work with them. It is accepted. C-Note then uses his brains to figure out the escape plan. Once he finds the loose cement in the shack, he knows of the escape plan.
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 marry Hector. Captain Bellick presses David to rat Michael telling everything he says. Michael tests the escape plan and informs the group that they are ready to go that night, but Lincoln was sent to solitary confinement protecting his brother.
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 because of her, and he replies that he does not understand how they have not killed her yet. Abruzzi meets T-Bag and asks him to forget everything, and they seal truce. Nika seeks out Sara and tells her life and how Michael helped her, but she actually steals Sara's key. A guy sees the Mustang in a junkyard where Aldo and Lincoln are hidden, but Kellerman bugs the conversation and goes to the spot. However, the police arrive and Captain Bellick arrests Lincoln, saving him from Kellerman. Sara seeks her key and recalls her meeting with Nika Volek; she calls maintenance service to replace the lock. Nick works for Abruzzi. Michael invites David and he betrays the plan to Captain Bellick. Lincoln is back to Fox River under 24 hours surveillance.
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.