As Lincoln Burrows awaits his fate on death row, his brother, a structural engineer convinced of Lincoln's innocence, gets himself incarcerated as well hoping to free his brother from the inside.
Michael seeks help of his fellow prison inhabitants to execute his escape plans.
When Michael reveals his escape plan to Sucre, Sucre chooses to be no part of it, and requests a cell transfer. Michael gets a new cellmate nicknamed Haywire, who never sleeps.
Veronica keeps uncovering new information regarding Lincoln's case and decides she wants to work on the case full-time. When no one wants to help her on the case, Nick Savrinn (an attorney) offers his assistance and the two of them visit Lincoln.
Kellerman and Hale blackmail Warden Pope. Michael finds out he might get out earlier than anticipated. Veronica becomes uncertain of her allies.
Michael creates a lock-down by sabotaging the air conditioning in order to execute his breakout plan properly, and unintentionally causes a riot that gets Sara into huge trouble. Meanwhile, an ex-con is blackmailed into seeing to that Lincoln is killed.
While the riot intensifies, Abruzzi and Sucre join forces. Michael must decide whether or not to save the life of Dr. Tancredi.
Michael finds out a storeroom fundamental to his escape plans has been converted into a break room. Veronica and Nick are being threatened.
Abruzzi's demotion in the prison hierarchy puts the entire escape plan at risk. Michael finds himself in the position of trying to protect T-Bag's new "fish" and facing the threat of T-Bag exposing the plan to the guards. The inmates dig themselves into a hole.
Michael is forced to give up Fibonacci's location to Philly Falzone, and Kellerman and Hale get a little unwanted help to track down LJ who has gone missing. Veronica and Nick uncover evidence against the man Lincoln was convicted of murdering.
The escape gang and Dr. Sara are shocked when they learn the identity of Michael's latest visitor, who brings with her a priceless piece of the plan; Bellick's suspicions are aroused; Tweener's pickpocketing skills get Michael back some valuable time. Quinn tracks Veronica, Nick and LJ to the cabin in the woods and Kellerman and Hale have a life-threatening difference of opinion.
With proof that his escape plan is working, Michael gets suited up to overcome the vertical limits of his last obstacle. Back in PI, as the escape attempt draws near, the group tries to reduce their number by one and targets T-Bag, who has some insurance in his pocket. Outside the prison walls, LJ slips away to attend his mother's funeral, which is also attended by her murderer. Veronica gets a call from an unlikely source who sheds light on the night of Terrence Steadman's assassination.
With Lincoln’s execution scheduled for the following day, Veronica comes out of hiding to reach out to him and gains a newsworthy ally in the process. Kellerman makes the ultimate sacrifice to preserve the conspiracy. Michael must find a way to get Lincoln out of Solitary confinement in time for the escape that evening. The inmates risk everything as they attempt the escape.
A CO and his supervisor notice that the utility room's frosted glass door has been broken. They do some investigation and find two pieces of broken pipe. Nick and Veronica ask a judge to grant a stay of execution for Lincoln. In the meeting, there is also a man named Peter Tucci who presides over Respondent's table (aka makes it his mandate to destroy Nick and Veronica's case). Sucre and T-Bag face off during rec time. Sucre is sick and gets a guard's sympathy. Lincoln demands to see Michael but Stolte denies it.
A face from the past haunts Lincoln on his execution day; Veronica raises the dead to prove Lincoln's innocence; Michael takes guard duty in formulating a new escape plan; and a mystery man sheds light on the conspiracy.
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.
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.
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.
Dr. Sara 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 wall, who will be left behind and who will leave the prison in a body bag.
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.
Picking up eight hours after their escape from Fox River, Michael, Lincoln, Sucre, Abruzzi and C-Note are on the run for their lives as a vengeful Bellick leads the prison guards seeking to capture their escaped quarry; Dr. Sara is in critical condition from her overdose; Veronica finds herself a prisoner with Terrance; T-Bag tries to get the upper hand while fleeing from the authorities; and a new take-charge FBI investigator proves to be Scofield's match.
Abruzzi, Sucre and C-Note make a run for it on their own; Michael and Lincoln plan another breakout this time to rescue a jailed LJ, whom Mahone targets in his quest to capture the escaped cons; Bellick and Warden Pope face a jury of their peers regarding the prison escape; Tweener hitches a ride with the college crowd; and T-Bag takes drastic measures to get the upper hand.
Mahone zeroes in on Michael and Linc's car, which was towed to a Chicago lot, but Michael gets there first. Unfortunately for the brothers, the backpack containing their fake IDs isn't in the vehicle. Elsewhere, Sara is released from the hospital, but that's not good news, especially after a difficult meeting with her father; Sucre and C-Note are determined to get to their loved ones, no matter what; and Bellick and Geary go into the bounty-hunting business together.
Bellick and Geary catch up to Michael and Lincoln. Abruzzi surfaces in Brooklyn with plans to flee to Sardinia, but first makes a side trip to D.C.
T-Bag stops at a gas station, where his vehicle attracts attention. Tweener and Debra Jean hit it off as they head off to Utah, and Kellerman strikes up a conversation with Sara after the NA meeting.
Michael and Lincoln search for Westmoreland's hidden money in Tooele, Utah. Sucre goes to Las Vegas to stop Maricruz from marrying Hector. Maricruz's sister tells Sucre she'll arrange for the two of them to be alone together, but instead calls the cops. Mahone picks up an interest in the legend of D.B. Cooper and then receives a mysterious package. Kellerman gets one step closer to Sara.
Michael and Lincoln go house-hunting in Utah to find Westmoreland's hidden money; T-Bag shows his particular brand of Southern hospitality; Haywire finally re-surfaces; Sucre finds a familiar face on the road; Mahone's interest in the legend of DB Cooper leads him closer to the escapees.
Lincoln is determined to reunite with LJ, who is suspicious of his good fortune in Arizona; Michael, C-Note, Sucre and T-Bag's hunt for buried treasure finally pays off; Kellerman has a change of heart just as Sarah is targeted by The Company; and Mahone forces Tweener to make a deadly choice.
The fugitives again split up as they scurry out of Tooele, but only one has the money. Later, Bellick and Geary arrive and question Jeanette Owens. In Arizona, Linc watches as LJ is freed from lockup. And in Chicago, a Reynolds thug barges in on Sara, while Mahone must answer for the deaths of Abruzzi and Tweener.
Michael looks up Mahone's ex-wife and discovers something telling about his pursuer. And Sara figures out what the numbers on the origami birds mean, learning where to meet Michael in the process. Trouble is, so do Kellerman and Mahone. Linc and LJ head for the rendezvous point, too. Meanwhile, C-Note returns to Chicago for a rendezvous with Kacee and Dede, but Lang gets to them first; and T-Bag seeks out Ms. Hollander, but stops first to buy some flowers.
Michael and Sara find each other in New Mexico, but Mahone finds them both. In Arizona, Lincoln and LJ get into another auto wreck. And in Nebraska, Sucre tries desperately to get in touch with Maricruz by phone.
While Michael makes his way to a rendezvous with the plane and, he hopes, Lincoln, Mahone remains in the factory where Michael left him, but not for long. Meanwhile, Linc has to say good-bye to LJ again; Sara is in a tight spot, and T-Bag gets out of one, but he leaves something behind.
With Mahone on Michael’s trail, he has to take time for a sad farewell. C-Note takes a risk to go out into the public. Bellick has a stunning confession. Michael and Lincoln make their final flight for the border.
Mahone catches up with Michael and Linc, but the border patrol arrives at the scene before he can shoot them. This is bad news for Mahone and Kim, but not for Kellerman. Meanwhile, T-Bag needs a new hand as he searches for Ms. Hollander, and he finds other female companionship; Bellick is denied bail and is running out of options, as is Sara; and Sucre must take a leap of faith when the Feds lock on to the plane carrying him to Mexico.
This special highlights major events from both seasons 1 and 2.
Lincoln and Michael are on the run with Kellerman as they figure out how to take the fight back to "The Company". Meanwhile an injured Agent Mahone decides he's done working for "The Company" but his decision has bad repercussions. Back at the prison, Bellick gets a taste of the medicine he gave out when he was the Captain.
Michael, Lincoln and Kellerman take the airwaves hostage as they attempt to evade the authorities and get a message to a missing Sara; Bellick gets a surprise visit in Fox River’s infirmary; Haywire resurfaces and lands in more trouble; Sucre takes his good Samaritan for a ride
Michael and Sara become more than "strangers on a train" en route to confronting the President; Mahone recruits an new ally in his attempts to capture the fugitives; T-Bag puts on a happy face when the welcome wagon arrives; and a fourth escapee takes a fall.
Michael and Sara realize that Warden Pope is the key to recovering information that will bring down The Company; Mahone corners another escapee; C-Note fears for his daughters life; Sucre learns the dangers of hitchhiking en route to reuniting with Maricruz; and T-Bag walks down memory lane when he takes the Hollander family to his childhood home.
A psychologist helps T-Bag dig deep to find his 'nice side'. Sarah, Michael and Lincoln find the evidence needed to bring down The Company, while Kellerman is closing in on the location of the President.
As Kellerman prepares for an assassination, Michael is determined to confront the President and expose her secrets recorded on the audiotape. Mahone plays a tense waiting game with Sarah. T-Bag's lost luggage may prove a windfall for Bellick and Sucre. C-Note's drastic actions leave him hanging.
Sarah weighs sacrificing herself in order for Michael and Lincoln to set sail to freedom; T-Bags reign of terror continues south of the border as Bellick forces Sucre to track down the missing money; Mahones actions finally catch up with him; and an escapee finally tastes freedom.
Michael is determined to get his hands on T-Bag as much as Bellick is determined to get his hands on the millions; Lincoln and Mahone square off; Sarah faces judgment day as Kellerman decides his own fate.
Michael races against the clock to rescue Lincoln and beat Mahone at his own end game; Sucre risks his life to save a missing Maricruz; Kellermans testimony at Sarahs trial proves deadly; and T-Bag and Bellick find themselves up a Panamanian river.
The season opener finds Michael Scofield in Sona, a hellish and deadly Panamanian prison where a previous riot has forced all authority out and has left the prisoners in charge of their own lives (and deaths). With the fate of his loved ones hanging in the balance, Michael must to find Whistler, a mysterious fellow inmate hiding within the prison's sewer system, in order to break him out from a prison from which there is no way out. Meanwhile, Lincoln searches for a missing Sara and receives troubling news about LJ.
After Michael gets bad news from Linc, he sets out to find a prisoner named Whistler, who holds the key to his freedom. That's easier said than done: Whistler is hiding in Sona because there's a price on his head, and Lechero is not about to help Michael find him. In addition, both Mahone and Bellick want to get to Whistler too. Meanwhile, T-Bag won't allow a little humiliation stop him from insinuating himself into Lechero's good graces.
Someone slides an envelope containing a photo of Sara and LJ under the door of Linc's hotel room. It might contain clues to their whereabouts. The Company Operative in Panama City might help, too, but Linc must persuade her it's in her best interest to do so. And at Sona, Michael gets to know Whistler; Lechero begins to lose confidence in his ability to shape events; and Mahone, who is in increasing need of his medications, meets the lawyer who'll defend him.
After failing to rescue LJ and Sara, Linc receives an ominous warning from the Company; Michael plans an electrifying escape from Sona; a face from the past haunts Mahone; T-Bag crawls up the ladder while Bellick lands in hot water with Lechero.
A new inmate enters Sona, unnerving Whistler and raising Michael's suspicions; Linc plans an ocean getaway with Sofia as Susan moves up the escape timetable; T-Bag tempts his fate with his latest attraction; and Sucre attempts to get the goods into Sona.
Whistler becomes the prime suspect when an inmate is found murdered, leaving Michael to prove his innocence. Michael also wants proof that Sara is still alive or he will refuse to help Whistler escape. Meanwhile, Linc and Sofia watch the routine of the morning guards, and Mahone receives an offer to get him out of Sona.
Susan takes the escape into her own hands; Lechero reveals a secret buried beneath Sona; Sofia uncovers more of Whistler's past; Mahone's freedom hinges on his testimony.
Michael hopes to talk his way out of solitary confinement, while Bellick gets himself into trouble after refusing to mop up a mess. Meanwhile, Susan B. has her sites set on Sucre
as he makes a delivery to Sona. Sofia confronts T-Bag after he makes an offer to Whistler. Also, a mysterious American woman has arrived in Panama in search of Michael.
The battle for control of Sona comes to a boil between Lechero and Sammy as T-Bag enlists Bellick once again to display his fighting skills. Meanwhile, Michael returns to shore up the escape tunnel, and in Panama City, a search is performed by Linc on "Gary Miller," while Sucre and Susan B. have a pair of meetings.
Lechero, Whistler, Mahone, Bellick and T-Bag all decide to follow Michael when he begins again to tunnel out of Sona, but working as a team may be a problem. Linc and Sucre assist when the weather causes some last minute changes in their plans. Back in Panama City, Sucre is threatened by Susan B. with the worst thing imaginable. She also longs to see Sofia again.
The escapees find success for some, if not all in their attempt, and are assisted by an unexpected source. But a mistake finds one escapee leaving behind something.
Michael and Linc meet up with Susan B. as the make their way into Panama City, minus Whistler. Meanwhile, Mahone waits at a Panama City cantina for an appointment, while a roadblock is setup on the way out of the country which stops McGrady and his father. Back at Sona, Sucre pays for attempting an escape, while T-Bag aids Lechero as he takes a look at the new landscape beyond the walls.
Michael uncovers unbelievable news in Los Angeles when he seeks revenge against Whistler and Gretchen for Sara’s death. Michael and Lincoln are reunited with the gang and receive an offer from a Homeland Security Agent they cannot refuse. Mahone suffers a devastating loss, and T-Bag is deserted during his flight to freedom.
Michael, Lincoln, Sara and the team work with Roland, a new team meber, to get a copy of the data card. Meanwhile, Wyatt continues his mission to track down the brothers while T-Bag makes his way north using the bird book as his guide.
Michael and the team have one day to find the next cardholder or they risk going back to prison. Mahone seeks revenge on Wyatt who is attempting to extract info on Sara’s whereabouts, while T-Bag finds the gateway to his new identity and future.
Michael, Lincoln and Sucre must crash a police benefit to obtain the next card key. Reeling from another death, Sarah falls back into an old habit. T-Bag arouses suspicion and runs into some old “friends” his first day on the job.
Michael and Lincoln make their way to the Treasury Department in search of the next key card holder; an awkward alliance formed by T-Bag at his new job arouses the suspicions of Sucre and Bellick; Wyatt uses his magic touch on Gretchen.
Michael and the team tracks a key card holder to a racetrack; Mahone gets caught with something priceless; Wyatt targets Agent Self; T-Bag starts to figure out Whistler's code.
Lincoln takes members of the team to Las Vegas where Sucre gets an indecent proposal. Sarah learns about Michael’s condition, and Roland pushes his luck too far. Gretchen teams up with T-Bag who makes an offer to Michael he cannot refuse.
Meanwhile, the secrets in Whistler’s bird book are finally revealed.
Lincoln hatches a plan to get the final card from the General. Meanwhile, Michael and Self must work with Gretchen and the group continues to harass Roland for losing the device in Vegas.
Wyatt gets a taste of his own medicine, and Mahone finds some resolution. T-Bag scrambles when the police investigate his missing co-worker while Gretchen gets cozy with a Company man.
Michael’s condition continues to worsen, and a team member makes the ultimate sacrifice while planning the underground break-in for Scylla.
When Michael's condition begins to worsen, Sara has no choice but to take him to the emergency room. Later, Sara receives a shocking call about Michael's ailment. Meanwhile, Sucre and Lincoln find themselves in explosive territory; Agent Self makes a surprising ally; and Mahone is able to track down vital information about Scylla.
Michael and the team find themselves in a race against time, but Michael's deteriorating condition forces Sucre to take the lead in the break-in. Meanwhile, Gretchen tries to get the last key card from the General, and T-Bag is faced with a decision that could take him away from his criminal life for good.
As the search for Scylla comes to a surprising end, Sarah takes a hostage, T-Bag and Gretchen have their last stand at Gate, and Michael and Lincoln are betrayed by one of their own as they finally get to go face-to-face with the General.
It's up to Michael to hold the gang together after they find out they were betrayed by one of their own. Meanwhile, Gretchen is blackmailed by T-Bag's new partner.
Michael and Lincoln work to get Scylla back from Gretchen and her new partner. Meanwhile, Mahone meets up with an old colleague, and T-Bag is put to the test.
Michael gets medical attention from the most unlikely of places, and Westmoreland returns to help uncover the true meaning of Scylla. Meanwhile, Lincoln and Sucre race to stop Gretchen before Scylla is lost forever.
Lincoln and his new partners arrive in Miami to recover Scylla from its shocking new owner, and Sara searches for a missing Michael who learns some surprising information about his past. Meanwhile, a double-crossing leads to a death and an arrest.
Michael and Sarah learn the dangers of hitchhiking as they make their way to Miami, and Lincoln meets with Christina who informs him of her plans to take over the Company.Meanwhile, Pad Man feels the heat from an new enemy, and T-Bag and Self’s search for Scylla leads to an unexpected discovery.
Michael and Lincoln square-off over Scylla as Christina orders a kill shot and set sets her plan in motion. Sarah receives some unexpected news, T-Bag causes a scene at the Indian Embassy and Pad Man’s paranoia leads to a death.
Michael has an uneasy reunion with Christina, who drops a bombshell regarding Lincoln. Lincoln races to stop Christina’s deadly master plan. T-Bag must prove he is a Company man.
Pandemonium erupts at the hotel following the assassination, and Christina puts the final pieces of her plan together. Meanwhile, the General makes good on his threat, and Michael is forced to choose between saving either Lincoln or Sara.
Familiar faces return to help Michael end his quest to bring down The Company once and for all.