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.

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.

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.

Michael gains a necessary piece of information to effect his escape, but can he keep the Warden from kicking him out?

Michael's idea to get more drilling time by provoking a lock-down backfires horribly.

Michael saves Dr. Tancredi from the rioting prisoners, but Lincoln and Veronica are in need of their own rescue.

Veronica, Nick and LJ must go into hiding, while Bellick unwittingly provides Westmoreland's motivation to aid the escape.

With Abruzzi becoming more desperate to regain authority within the prison, it seems that Fibonacci's number is up.

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 year 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 West and makes 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, reporting 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?

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 solitary confinement and Michael tells to his partners that he has completed the map, but he needs the key to the infirmary. Abruzzi is back to Fox River, apparently converted into 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 up. Michaels asks for help from Nika. Veronica finds many calls from Montana on Quinn's phone. 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 make a truce. Nika seeks out Sara and tells her about 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.

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

It is the morning after their escape from Fox River, and the inmates narrowly avoid being caught by Bellick as they jump onto a freight train. FBI Special Agent Alex Mahone has been assigned to their case and calls a press conference urging the public to turn in the "Fox River 8." Michael, Lincoln, Abruzzi, C-Note, and Sucre encounter a hunter and his daughter. He holds them at gunpoint until Abruzzi grabs the daughter and forces the hunter to give them his SUV and let them go. The escapees head for a location where Michael has things stored. Agent Mahone tracks Michael's credit card to a storage facility in Oswego, but quickly figures out that one of Michael's tattoos holds the real location. Michael's tattoo "Ripe Chance Woods" is a clue pointing to a cemetery where Michael has items buried in the grave of "E. Chance Woods." Just two steps behind, Agent Mahone arrives at the scene just as the inmates have gathered what they need. In the meantime, T-Bag discovers a veterinary clinic and forces the Vet to re-attach his severed hand. Dr. Sarah Tancredi recovers from her overdose. Inside her purse, she finds an origami swan left for her by Michael with a message, "There's a plan to make all of this right", and a code. The code is a series of numbers which reads 3221243324 for the first line, 4221312231 for the second, and 23133121 for the third. Veronica locates Terrance Steadman in Montana, and finds that the doors are locked from the outside, holding him hostage (albeit willingly). Veronica calls 911, and then talks to Lincoln and tells him what she has learned. Employees of The Company arrive and kill Veronica for having unraveled their plot and for having found Steadman. Lincoln hears Veronica's final words as she dies, and is consumed with grief. Mahone studies Michael's tattoos, and feels that they are the key to finding the escapees.

The F.B.I agent Mahone decides to use L.J to get to Michael and Lincoln by cutting a deal with him and making him trick the two fugitives into revealing their location. Michael and Lincoln decide there's only one thing they can do, rescue L.J in a daring raid at the county jail. Only one problem though, Mahone is personally guarding L.J and won't let him out of his sight.

In Maljamar, New Mexico, Michael takes what he needs from a sporting-goods store, then has a crisis of conscience. In Tribune, Kansas, T-Bag narrowly escapes the police but has to leave his hand behind. In Trinidad, Colorado, the three Burrowses discuss politics, but face an unexpected threat. In Gila, New Mexico, Kellerman ties up Sara and resolves to get what he needs from her. Mahone meets Kim for the first time. Bellick receives treatment for the blow to his forehead, and interacts with a local police detective.

Michael Scofield and Sara Tancredi fail to get the tape from the Corona de Oro cigar club in Chicago, where security was at the ready, and turn to former warden Henry Pope, a club member, but he wants to call the police. Michael draws his gun and hands it over to prove his veracity; Sarah convinces him to go in with her late father's humidor key and he finds a computer memory stick. In Mexico, Fernando Sucre has car trouble and gets a ride from an Ixtapa airport security employee who sees his wanted-poster just after they parted at the airport, so he must run with his bride. T-bag and his forced-along family find his own house vandalized and looted except for the family bible, which arouses in him youth memories of his perverted father, and assures Suzy he wants their love and is happy to be infertile, her bloodline should take the Bagwells's place. When she refuses, he locks them up, considers ax-murdering but just leaves them behind. FBI Special Agent Alexander Mahone has tracked down Benjamin Miles 'C-Note' Franklin and his daughter, but lets them escape in a bus rather than shoot the kid. C-Note brings her to a doctor, worried about the kidney disease PKD, but won't allow inserting a catheter, rather turns himself in to Mahone, who is with his own boy in Colorado, and makes a deal to get him Scofield. Pope is out of the club, but is greeted at the entrance by Secret Service Special Agent William 'Bill' Kim whom only Paul Kellerman, watching from a roof with Linc, knows by sight. Michael drives over Kim and gets away with Pope, Sarah and Linc, locking Kellerman out. When Michael tells the others he's prepared to honor his promise to Pope (which the others didn't know about) to turn himself in for his help, Henry hands him the stick and lets them go.

Michael gains a necessary piece of information to effect his escape, but can he keep the Warden from kicking him out?

Michael Scofield and Sara Tancredi fail to get the tape from the Corona de Oro cigar club in Chicago, where security was at the ready, and turn to former warden Henry Pope, a club member, but he wants to call the police. Michael draws his gun and hands it over to prove his veracity; Sarah convinces him to go in with her late father's humidor key and he finds a computer memory stick. In Mexico, Fernando Sucre has car trouble and gets a ride from an Ixtapa airport security employee who sees his wanted-poster just after they parted at the airport, so he must run with his bride. T-bag and his forced-along family find his own house vandalized and looted except for the family bible, which arouses in him youth memories of his perverted father, and assures Suzy he wants their love and is happy to be infertile, her bloodline should take the Bagwells's place. When she refuses, he locks them up, considers ax-murdering but just leaves them behind. FBI Special Agent Alexander Mahone has tracked down Benjamin Miles 'C-Note' Franklin and his daughter, but lets them escape in a bus rather than shoot the kid. C-Note brings her to a doctor, worried about the kidney disease PKD, but won't allow inserting a catheter, rather turns himself in to Mahone, who is with his own boy in Colorado, and makes a deal to get him Scofield. Pope is out of the club, but is greeted at the entrance by Secret Service Special Agent William 'Bill' Kim whom only Paul Kellerman, watching from a roof with Linc, knows by sight. Michael drives over Kim and gets away with Pope, Sarah and Linc, locking Kellerman out. When Michael tells the others he's prepared to honor his promise to Pope (which the others didn't know about) to turn himself in for his help, Henry hands him the stick and lets them go.

The F.B.I agent Mahone decides to use L.J to get to Michael and Lincoln by cutting a deal with him and making him trick the two fugitives into revealing their location. Michael and Lincoln decide there's only one thing they can do, rescue L.J in a daring raid at the county jail. Only one problem though, Mahone is personally guarding L.J and won't let him out of his sight.

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.

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?

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

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.