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 hands over an address to Falzone, allowing work to resume on the tunnel. Meanwhile, the VP enlists the help of a dangerous specialist.

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.

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.

With hospitals and clinics under surveillance, Michael brings Lincoln to Nika's home to heal his wounded leg. Then he returns to the place where he parked his Accord and finds that the car has been towed. Meanwhile agent Mahone retrieves Michael's backpack with his passport from a vagrant that broke the rear window of Michael's car to steal the backpack. Michael goes to Brewster Towing yard to recover his car. Meanwhile Sucre finds that Maricruz will marry Hector in a couple of days and he heads to New York in a stolen car. Sara is arrested and her father visits her, pays her bail and orders her to tell a fake version about the incident in Fox River since he will be the next Vice-President of United States. Later she goes to rehabilitation where Kellerman is pretending to be an addicted patient. C-Note schedules a meeting with his wife, but his conversation is bugged by agent Mahone. Bellick and Geary meet each other by chance and later they team-up to get the $400,000 reward for capturing Michael and Lincoln. They go to Fox River and Bellick interrogates Manche Sanchez, who discloses the plan of the fugitives. Michael and Lincoln forge a car accident to escape from Mahone, but they do not see that Bellick and Geary are in their tail.

Michael, Linc, and Nika are captured by Bellick and Geary, who intend to retrieve Westmoreland's money in Utah. Tweener continues his drive with Debra Jean. Abruzzi is reunited with his wife and children and is set to flee the country with them, but decides to take care of Fibonacci first. T-Bag has a close call with the police at a Nebraska gas station, and then poses as a Marine who lost his hand in Iraq. Mahone waits for confirmation of the deaths of Michael and Linc in the car explosion, and meanwhile gets a lead on one of the other fugitives. Kellerman (posing as a recovering addict named Lance) befriends Sara.

In Cutback, Montana, Kellerman lures the police and Michael and Lincoln abduct the cameraman Greg of Fox News and succeed in escaping from the siege. Michael and Lincoln decide to tape a message to be released in the Breaking News. Mahone is back in Chicago and analyzing the message; he interrogates Greg and he tells that he had overheard Michael tell that they should cover 460 miles in six hours. Mahone deduces that they intend to meet President Caroline in Denver. Wheeler discusses with Mahone and yells that the Internal Affairs department asked him to follow all moves of Mahone. Bellick is badly wounded in the infirmary of Fox River. Sucre befriends an old passenger in a bus to Ixtapa; however the driver asks him to leave the bus in a small town and Sucre robs the Volkswagen of the old man. In Algoma, Winsconsin, Haywire befriends a young couple and the girl has bruises on her arm; she tells that her abusive drunken father beat her.

Linc finds Michael is gone from their Christina Rose yacht after receiving Sucre's message (also intercepted by Mahone, who thinks to have found his way out); scary scumbag T-bag is in Panama City's Fin del Camino hotel with the money. A fire-cracker he pays a local boy to plant shows Michael Mahone's two plants on the plaza, but Bellick pulls his gun on him, accompanied by Fernando who denies sending the message. Scofield smells a trap and states their goals: money for Bellick, Maricruz for Sucre, T-bag for him, then reminds Fernando in private Maricruz is his legitimate priority, not revenge. Sarah Tancredi's trial proceeds, and the judge allows showing Michael's tape clearing her; her lawyer advises her to take a twelve-year plea, in effect nine years in hard security. When T-bag leaves, Mahone's two men tail him, followed by the escapee trio. Mahone is suddenly attacked by Lincoln who calls him the murderer of his dad. The trio surprises and disarms Mahone's duo which carries no FBI-identification, and next T-bag, but hears police sirens outside. After lining up his medals and putting on his uniform, Paul Kellerman shoots himself in the head, but his pistol jams; his sister insists it's a sign to make a new start in life. He goes to testify on Sarah's behalf. Instead of money, Fernando finds a girl shot, T-bag makes a run past Bellick while police enter; Michael and Sucre follow over the fire escape, a car slightly running into him causes T-bag to be caught again. He deals with Michael to trade his escape, without the money, for information but Scofield decides to dump him at the embassy. The monster finds a screw driver, stabs Fernando and thus causes a car crash, allowing him to run with his precious backpack. Sucre insists Michael run after him in a palm wood, till he makes a stand with a knife. A broken bottle allows a fight. In no time Michael has the knife at T-bag's throat, who taunts him but still gets stabbed- in the arm, so the police can easily take him in. . .

Michael and the team have one day to locate the next cardholder or they risk going back to prison. Meanwhile, Mahone seeks revenge on Wyatt.

Dangerous threats keep Michael and Lincoln fighting to protect Sara and Mike. Meanwhile, Poseidon continues to try and outsmart Michael and the rest of the gang, which leads them to the ultimate showdown, and not everyone makes it out alive.

Michael, Linc, and Nika are captured by Bellick and Geary, who intend to retrieve Westmoreland's money in Utah. Tweener continues his drive with Debra Jean. Abruzzi is reunited with his wife and children and is set to flee the country with them, but decides to take care of Fibonacci first. T-Bag has a close call with the police at a Nebraska gas station, and then poses as a Marine who lost his hand in Iraq. Mahone waits for confirmation of the deaths of Michael and Linc in the car explosion, and meanwhile gets a lead on one of the other fugitives. Kellerman (posing as a recovering addict named Lance) befriends Sara.

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.

Michael hands over an address to Falzone, allowing work to resume on the tunnel. Meanwhile, the VP enlists the help of a dangerous specialist.

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

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.

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.

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

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

Michael and the team have one day to locate the next cardholder or they risk going back to prison. Meanwhile, Mahone seeks revenge on Wyatt.