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.

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 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 his efforts to try to get hold of all of the money Sucre runs into some unexpected difficulties. And Captain Bellick and his partner have not given up on finding their old inmates.

Michael tries to retrieve an item from Blanding Botanical Garden in Utah, but Mahone's people got to it first. Mahone believes that someone on his team is leaking information to the press; meanwhile Michael does some research on Mahone at an Internet café, then makes a trip to Durango, Colorado, to see a woman there. Linc and L.J. are on the road in Arizona. C-Note is in Chicago, and Agent Lang tries to use his wife to capture him. Bellick and Geary phone C.O. Patterson, at Fox River, to get information on where they should look for T-Bag. Sara is at a motel in Elgin, Illinois, trying to crack Michael's code. T-Bag arrives in Tribune, Kansas, for (as he puts it) "romance". Kellerman is on the trail of Sara.

Captain Bellick tortures T-Bag for the money during which T-Bag swallows the key and Bellick uses dirty tricks to get the key out.Bellick and Mac leave T-Bag on the boundary of the police.Sarah and Michael Scofield meet,but they are constantly chased by Alexander Mahone.Michael gets close to Mahone's helplessness.Meanwhile Lincoln Burrows and LJ are rescued by Lincon's dad but they are still not shielded from the dirty political games. Sucre tries to contact Maricruz but that plan fails because of the state police doing rounds.

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.

Picking up from where we left off, Sucre, Michael, Linc, and Aldo are together, with Mahone on their trail. Sara is face-down in the bathtub as Kellerman prepares to dispose of her body. C-Note is in Harvey, North Dakota with Kacee and Dede, who needs her medication. In Tribune, Kansas, Detective Slattery questions Bellick.

The Border Patrol arrests Michael and Lincoln, saving them from Mahone that claims that wants his life back. Sucre crosses the border and jumps in a parachute in the Sonora Desert in Mexico. T-Bag goes to a war veteran bar in Pratt, Kansas, and steals a prosthetic job from a veteran sergeant. Michael and Lincoln are apprehended in the Border Patrol Holding Facility, in Las Cruces, New Mexico, waiting for transportation to Fox River, but Bill Kim orders Mahone to kill them. T-Bag meets Denise, who works in the post office, and seduces her to get Susan Hollander's address. Bellick is sent to the District Court in Greeley County, Kansas, and has his bail denied. He makes a deal to be sent to Fox River expecting to have a good life. However the new warden decides to use him as an example of the new administration. Meanwhile Mahone tries to transport the prisoners, but the standard procedure does not allow it. Kellerman makes an arrangement to intercept the convoy in a blocked tunnel to kill the prisoners. However, Michael and Lincoln and helped by a surprising allied. T-Bag finds Susan.

Linc and Michael have decided to take the keys and escape, figuring at least they'll go down fighting. FBI Special Agent Alexander Mahone chased them while staying in contact with Secret Service Special Agent Paul Kellerman who suddenly shot Mahone and gave the brothers a ride because he wants revenge on the White House; Linc wants his instead, but is offered the location of Terence Steadman. T-bag visits his ex-girlfriend, who tells him the children think he's their Uncle Teddy on an oil rig, but he moves in; when she goes for a gun, he attacks her and her son attacks Zach him, so he turns the home into a private prison. In prison, former boss Bellick, who naively had made a deal in order to do his time in Illinois, shivers in general population among the prisoners he abused and their mates, he has none as the new warden sees him as an example of his new, clean ship; he soon realizes there's no pleasing them, and tries hitting hard; a loyal guard warns him the night shift is on his enemies side as he treated them badly. Benjamin Miles 'C-Note' Franklin tries to save his Kacee who is in custody, advising her to put all the blame on him; after hearing how scared his girl is, he asks one of his friends for help to run while she's on bail but the judge refuses bail. Mahone awakes in hospital, and reports to Kim on Kellerman's betrayal and the brothers' escape, which is hitting the TV news, but refuses to play anymore, even if that means jail; when his wife Pam phones their son is hurt he rushes out for Colorado, but is stopped to hear it's a warning to force him back in line; however he is through doing Kim's bidding and shoots his man. Kim calls Steadman's bodyguards: he must be evacuated to a safe house as Kellerman knows his residence, but he is already there with the brothers- Kims orders to kill everyone, but only the FBI men are shot; Kellerman explains Steadman is made unrecognizable, including plastic surgery, so their only option is to get him to Washington, where FBI agents who know can still make the truth stick. Michael decides instead to turn himself in while informing the press, despite Kellermans gun aimed at him, but Steadman prefers to commit suicide, and his corpse is worthless for the brothers.

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.

Sara meets Michael and Lincoln in a train station in Evansville, Indiana; when she sees Kellerman with them, she becomes disturbed and upset. Kellerman tells that she has a key of a private cigar club in Chicago. Caroline calls Kellerman and he tells that he is heading to Chicago by train, and she promises his life back, inclusive the chief of staff position. T-Bag tells Susan that they are passing through an "adjustment period" in their lives; when she tells him that she will have a guest called Patty Wallace, T-Bag welcomes Patty with a magnificent family brunch and uses the strong father figure to discipline Zack, seducing the guest with his charm and attitude. Wheeler is reporting the actions of Mahone to the FBI Headquarter and they find that Haywire killed a man in Algoma, Wisconsin. Mahone visits Bellick in River Fox, releases him using a habeas-corpus to make his dirty work, and gives a car, a pistol and an FBI badge to the despicable man. Bellick chases and traps Haywire, and waits for Mahone. In Benson, Minnesota, C-Note and Dede are leaving a snack bar when an addicted thief announces a heist. When Kellerman sees a road block on the train, he realizes that he was betrayed.

Captain Brad Bellick walks in the FBI office demanding Mahone pay him. Michael and his companions are impressed with the recordings on the stick, but it only helps if Kellerman's contacts in Washington use it right, notably high Justice official Cooper Green, who agrees to meet and cooperate, but is tailed by Kim's men. Linc calls his boy L.J., who refuses to give up his relatively normal life till further notice. Sarah meets Bruce Bennett. Bellick tries to bribe Sucre's incarcerated cousin into betraying his Mexican whereabouts. T-Bag finds therapist Dr. Stammel who looks like him, and murders him to steal his identity. Mahone is ordered to dispose of C-note for good once Kim believes he has Scofield; he promises to keep taking care of C-note's family, but only if he uses the content of a package he'll send to his cell- a noose. Sarah is too late calling Linc the real Cooper Green is in his office, but Michael tricks the fake one who pretended to be asthmatic just in time and knocks him down. Paul Kellerman visits his sister Kristine. Fernando Sucre is in heaven in bed with Maricruz Delgado when their baby kicks. The real Cooper Green could help with the tape, but then finds the memory stick has the copy date, not the recording date without which it is not admissible as proof, only to blackmail the president into signing a pardon.

C-note has jumped with the noose around his neck, but is saved by jailers; he has Mahone told he'll still do it. At a Chicago hotel, president Caroline Reynolds is expected for a speech. Michael sends the real Cooper Green away and agrees a meeting point with Linc and Sarah. Mahone enters Sarah's room and only pretends to fail looking under the bed to trap her, she pretends the brothers left her. In Mexico, T-bag finds Bellick is waiting at the luggage conveyor and must get his from the service side, but the laborer he knocks down falls onto it, so he must run. Lincoln surprises his old mate Derrick Sweeney and calls a favor: three tickets on a freighter for Panama. Kellerman is in position to shoot the fiendish president, but when she's in his sight Michael gets arrested just after shaking her hand, and is interrogated by Kim who demands to be left alone with him, to ask where Linc is, then tries literally to beat it out of him; the president barges in and sends Kim out just when he was about to shoot Michael; he tells her the tape is a delicate conversation she had with her brother after his 'death', and he still has copies at twenty locations. Fernando sees on TV T-bag is in Mexico and was videotaped trying to steal, so he deduces the $5,000,000 must be around and tells Maricruz he'll be right back; at his return only Bellick is there, armed and cuffs Sucre, in order to collect the reward, so Fernando offers to share the $5,000,000 by finding T-bag. Sarah guesses right Mahone is on an addictive drug. Caroline calls Linc, who plays the tape which proves her brother was alive on the isle of Terrence and hated conspiring with her Linc's faked conviction; Michael tells her about his suicide and dares her to make a decision: let him walk and sign a pardon for both brothers the very day, on live TV; Kim fails to stop him being released and walking out. When the phone rings, Sarah surprises Mahone and escapes- actually he arranged this and has her followed. Kim talks to a grim man in power; Reynolds announces on TV she has a malignant cancer and resigns immediately.

Now that Caroline Reynolds has stepped down as president, she can no longer sign a pardon, so the brothers must immediately disappear, forever. At the pier Sarah realizes she's being tailed and pretends on the phone already to be on board, so they sail without her while she is arrested. Lincoln stops Michael from returning for her. A week later, an FBI bigwig offers C-note a lesser sentence for testimony against Mahone, even freedom and witness protection for his family- bingo. Fernando grabs Bellick's gun while looking for T-bag, but Bellick shows a crucifix to prove he has Maricruz. The scumbag enjoys his fortune with a lady of the street playing his Susan-Q. The brothers arrive at Cristobal, Panama. Meanwhile Malone's team deduces Scofield's tattoos refer to Michael's mother Christina, presumably dead, and he presumes his computer contained much info on Panama for a reason. The man in power grills Kim on a small boat, and decides to change the strategy. Mahone sees through FBI-colleague Wheeler. C-note is reunited with his family and released. The brothers have a fight, torn by guilt for too many innocent people suffering through their well-meaning deeds, then board a yacht, named- Christina. Mahone tells Kim he's not happy with the results as he remains separated from his family, but is told he now needs help to escape, and therefore must go to Mexico- to help T-bag.

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. . .

Back at the yacht, Michael notices Lincoln is gone and calls him. Alex Mahone tells him Linc is no cold-blooded killer, so he was overpowered and hand-cuffed, and the ransom is the yacht and the fortune he assumes to be in it, to be agreed in five minutes. Now Mahone is even more wanted than the brothers. Kellerman's self-incriminating testimony and documents he brings get all charges against Sarah and Lincoln dropped, him arrested. Mahone calls Kim to fly over immediately. Alex calls his wife, to make her bring the kids for a holiday in her native Colombia, at Cartegena. Despite 30% blood-loss Fernado leaves hospital to report missing Bellick, who is already in jail and gets T-bag's company. Vendor Chaco gets Michael introduced to a local yacht owner to whom he suggests collecting the $100,000 reward on his head, then makes a better offer. Mahone called the police intending to frame the brothers for his intended murder on 'an Asian', but Michael refuses to hand over the money and Kim turns up early, with armed back-up. Mahone runs but is arrested. Kellerman knows the situation he is involved in and expects to be assassinated so his transport to prison is arranged to get car trouble and a masked man shoots him. Chaco delivers to the brothers, who got away with the money and intended to run and never look back, a crummy boat with a priceless surprise: Sarah and the great news for Linc, with good hope for Michael. Just then Kim turns up, refuses the money, aims at Linc and is shot by Sarah. Police arrive, chasing and trapping the trio. Michael takes the gun and pretends to take Sarah hostage, then lets himself be arrested and locked up in Sona. Malone calls his wife to forget he ever existed- from jail. T-bag expected to be released as agreed reward for baiting the brothers, but the man he hoped to bring him the good news says getting caught broke the deal.

Michael is once again imprisoned, but now in SONA (Panama), together with T-Bag, Mahone and Bellick. The prison is solely ruled by inmates, whose local prison-lord Lechero feels threatened by Scofield's 'fame'. Lincoln tries legal means to get Michael transferred, and gets a call from a relative. Both receive the same message, through different channels, from The Company.

After Michael gets bad news from Lincoln, he sets out to find a prisoner named James Whistler, who holds the key to his freedom. That's easier said than done: James 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.

Lincoln tries to save LJ and Sara. But he can't. Meanwhile, Michael has a phone conversation with Sara. And Lincoln gets a call from Susan B. saying that she put something in the garage for him.

Aftermath of Sara's death, Lincoln decides not to tell about it to Michael. Susan B. told Lincoln that if he does something wrong again, she's going to send pieces from LJ to him. Meanwhile, Sucre got a job in Sona. And Sofia starts to help Linc.

A test with a rat proves the tower snipers are very good, so Michael figures the only option to breaking Whistler out within 24 hours has to be at 3 PM, during the distraction of soccer game. Sucre accepts $5,000 from Lechero's cousin, Augusto, to smuggle a package into Sona. Linc is to arrange transport outside, but he and Sofia get turned away roughly by an army patrol two miles away. He tells her Sara has already been killed. He keeps it from Michael, as LJ is his ultimate priority. New prisoner Andrew Tyge is robbed to his boxers on arrival, and recognizes Whistler (who denies it), mentioning the McFadden, Nice in 1997. He is warned off by Mahone who has noticed Tyge snooping around Michael and Whistler. They plan an electric signal disturbance device to distract the guard tower. Before they can make a move, a reflection from the binoculars is spotted: the troops move in and find it in his cell. Michael admits it's his. When the commander is about to shoot him, Whistler claims it's his for bird-watching, and proves it showing the ornithology book (the one Linc couldn't hold on to).

Tyge tells Michael that he and Whistler were co-employees at the McFadden, a hotel in Nice, France. Mahone worries about Tyge's constant, keen observance of Whistler. Having to re-plan hastily, Michael tells Linc to find out the location of the nearby cafe and drug the guard's coffee, and also demands pictures of LJ and Sara before he escapes. Tyge is stabbed to death. Lechero questions McGrady and has Whistler dragged away for a confession. Michael believes Mahone and Bellick's denials. T-Bag offers Michael a ring he stole from Sammy (his rival for Lechero's confidence), to use to frame Sammy for Tyge's stabbing. Michael finds the murder knife under Mahone's bed and goes to Lechero to denounce Mahone, only to find he has just walked out of the prison. Agents Richard Sullins and Felicia Lang arrive at Sona to present Mahone with a plea bargain from the US Justice: a term reduction to 8 years for testimony against the government conspiracy and Lincoln. He could be out in 4 years, but Mahone refuses, now he faces life imprisonment. Lechero administers justice for Tyge his own way. Linc and Sofia succeed in drugging Captain Hurtado, but Susan finds out the brothers had a different timing planned and threatens LJ's life. With no recent pictures available, Linc confesses Sara's death, causing Michael to make a drastic decision.

Mahone is assured all he has to do is tell the truth, enjoying full immunity. Michael tells Whistler their row is part of a diversion, the escape is now or never, before the drug in the guard's coffee wears off. Just when the critical sun reflection blinds the other tower guard, they must wait and hide till Sammy has passed, but get through the cut bars. They climb down, but the glare disappears so they must climb back up as there is not enough time to escape. They get back in time and out to the courtyard, but Lechero refuses to allow them to cancel their duel to the death in the courtyard, which had been intended as a fake diversion. Sofia draws a gun on Lincoln to prevent him from turning Whistler over to killers. He retorts that's condemning an innocent L.J. to death. Guards wake the passed-out Captain Hurtado, see the climbing rope and storm into the prison. The Colonel shoots Papo, one of Lechero's crew, 'for not telling' and exposes his deal with Lechero, questioning if he's the right man for the job. Hearing the Sona siren, Linc flees by car and when Susan calls, he lies, telling her he has the 'escapees' in the trunk, but Pike, another company operative phones her: the roll-count was complete. Sucre stops her van by crashing into it, but even when Linc holds her at gun-point her accomplice won't trade L.J. He releases her and gets a short extension to find out what happened. Failing a hearing, Malone now believes Justice official Richard Sullins is setting him up to confess. Michael is dragged before Lechero, but not to be punished, he's ordered to take the fallen boss along when he and Whistler escape. Susan asks instructions from Whistler, he tells her - as Gretchen - to give the brothers four more days.

Lincoln tells Michael that they have four more days to rescue Whistler, but Michael is upset with his brother that he used him. Gretchen has a meeting with General and they decide to use power to release Whistler in an operation called "Bang and Burn". Later she asks Whistler to kill Michael. In Sona, the guards reinforce the bars in the windows, and Michael tells Lechero that this way it will be difficult to break-out. Sammy requests more men to Lechero to keep Sona under control. Sofia receives a call from Whistler's mysterious landlord telling that he has some "insurance papers" from her boyfriend, however, the Company intercepts the conversation. When Sofia receives the documents, she finds a passport of Whistler in the name of Gary Miller. But Gretchen arrives and takes the documents. Mahone tells Agent Lang how he killed Shales and then high from the pills, asks her to get some drugs for him otherwise he will not be able to speak in the hearing. T-Bag gives a message from Lechero with the blueprint of his cell with a hidden door and an access code. Whistler is ready to stab Michael when Lechero arrives and he hides the knife. Michael asks McGrady to request his father to call Lincoln and give him a message: "Don't come home for dinner." Mahone fails in the hearing and is sent back to Sona. Lincoln, Sucre and Sofia are attacked by the Company's agents and the brothers realize that something is happening, i.e., the Company does not need them anymore. When the "Bang and Burn" Operation begins, Michael catches Whistler and Gretchen fails in her intent. General Zavala has Michael hauled in for questioning over the attempted breakout.

After the helicopter fails to break out Whistler, Sona's new commander, General Zavala, decides to make Michael talk by putting him into a sun-exposed isolation hot-box. He promises to help in exchange for the truth, verifies the L.J. situation and is told it's about Whistler. Whistler, realizing the tunnel is a no-go without engineer Scofield, denies knowledge blatantly to Zavala and is threatened with torture, until he admits to collaborating with Michael, who convinces him to give up Susan/Gretchen's name. Meanwhile Lincoln, is given a short meet up with L.J. as motivation. Mahone is back in Sona, desperate without his drug. T-Bag and his allies are mainly concerned with Lechero's expected succession and another bare-knuckle fight, won by Bellick. Gretchen recruits Sucre as a double spy (or triple for Linc); then General Zavala arrests and tortures her. Only Whistler's admission makes her admit L.J.'s kidnapping and leads them there, but she manages to kill the General and escape. Michael and Whistler are returned to general population, Mahone and T-Bag join the tunnel escape party. Lechero's cousin Augusto, now calls on Sammy to open the package - a gun.

Sammy reminds Lechero that Papo is dead and presses Lechero to kill Michael. Lechero replies that he also wants Michael dead, but he does not want an uprising in Sona. Mahone receives a picture of his son through the mail. Lechero, Michael, Mahone, Whistler and T-Bag inspect the hole in the tunnel and Michael requests a saw and hammer to support the tunnel. Sammy takes the over the reign of Sona with the pistol delivered by Augusto and other three gangsters and promises a box of bottles of rum for the inmate that kills Michael. T-Bag convinces Bellick to give the chicken foot to Sammy, promising him a spot on the escape team. When Bellick discovers that there is no more acetone, he unsuccessfully tries to call-off the fight. Meanwhile Lincoln and Sofia visits Osberto and buy a bomb. Sucre plants the bomb under the seat of Gretchen's car but she unravels that, saying she found Maricruz tracking the US$ 25,000.00 check she gave to him. Sammy leaves the fighting with Bellick to chase Michael, who is locked behind the door in the tunnel with Mahone. Sammy beats Whistler, who was left behind, trying to get the combination of the door. Michael removes a wedge from the hole and the tunnel collapses over Sammy, burying him, while Lechero and Mahone kill the three other gangsters. Sofia finds a wallet hidden in Whistler's bag.

As Michael finalizes plans for the escape, his fellow plotters begin to turn on him. Meanwhile, Whistler ponders a betrayal when Sofia is threatened.

Michael, Whistler, Mahone and McGrady escape from Sona - but not everything goes according to plan, and the exchange is compromised.

LJ and Whistler are exchanged, but more surprises abound. Meanwhile, T-Bag's scheming finally pays off.

Michael, Mahone, Sucre and Lincoln try to get into the house where Scylla is being kept safe. T-Bag and Sancho head to San Diego in the desert.

The gang has to break into the well-guarded home of company man Stuart Tuxhorn. Elsewhere, T-Bag must go to extremes to survive.

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.

To get the next data card, Michael, Lincoln and Sucre must crash a police benefit. Meanwhile, T-Bag arouses suspicion on the first day at his new job.

The gang, with Don's help, must break into a safe at the Treasury Department to get the next Scylla card. Elsewhere, Gretchen manages to escape.

Mahone is arrested, putting the whole gang at risk - and Mahone squarely in Wyatt's sights. Meanwhile T-Bag's charade is discovered.

Lincoln, Sucre, Sara and Roland follow a Scylla cardholder to Las Vegas, where Roland has his device commandeered after he gets caught gambling.

A daring plan is hatched to get the final card from Pad Man, and an uneasy alliance is formed with Gretchen - but there's a traitor among the ranks.

The team needs to make their way through a 30,000-gallon water main to get to Scylla. Meanwhile, T-Bag fends off an investigation.

Michael collapses and must go to the hospital. Elsewhere, Sucre steps on a land mine, and Trishanne's surprising secret is uncovered.

The team needs to make their way through a 30,000-gallon water main to get to Scylla. Meanwhile, T-Bag fends off an investigation.

Michael collapses and must go to the hospital. Elsewhere, Sucre steps on a land mine, and Trishanne's surprising secret is uncovered.

To get the next data card, Michael, Lincoln and Sucre must crash a police benefit. Meanwhile, T-Bag arouses suspicion on the first day at his new job.

After the helicopter fails to break out Whistler, Sona's new commander, General Zavala, decides to make Michael talk by putting him into a sun-exposed isolation hot-box. He promises to help in exchange for the truth, verifies the L.J. situation and is told it's about Whistler. Whistler, realizing the tunnel is a no-go without engineer Scofield, denies knowledge blatantly to Zavala and is threatened with torture, until he admits to collaborating with Michael, who convinces him to give up Susan/Gretchen's name. Meanwhile Lincoln, is given a short meet up with L.J. as motivation. Mahone is back in Sona, desperate without his drug. T-Bag and his allies are mainly concerned with Lechero's expected succession and another bare-knuckle fight, won by Bellick. Gretchen recruits Sucre as a double spy (or triple for Linc); then General Zavala arrests and tortures her. Only Whistler's admission makes her admit L.J.'s kidnapping and leads them there, but she manages to kill the General and escape. Michael and Whistler are returned to general population, Mahone and T-Bag join the tunnel escape party. Lechero's cousin Augusto, now calls on Sammy to open the package - a gun.

A daring plan is hatched to get the final card from Pad Man, and an uneasy alliance is formed with Gretchen - but there's a traitor among the ranks.

Mahone is assured all he has to do is tell the truth, enjoying full immunity. Michael tells Whistler their row is part of a diversion, the escape is now or never, before the drug in the guard's coffee wears off. Just when the critical sun reflection blinds the other tower guard, they must wait and hide till Sammy has passed, but get through the cut bars. They climb down, but the glare disappears so they must climb back up as there is not enough time to escape. They get back in time and out to the courtyard, but Lechero refuses to allow them to cancel their duel to the death in the courtyard, which had been intended as a fake diversion. Sofia draws a gun on Lincoln to prevent him from turning Whistler over to killers. He retorts that's condemning an innocent L.J. to death. Guards wake the passed-out Captain Hurtado, see the climbing rope and storm into the prison. The Colonel shoots Papo, one of Lechero's crew, 'for not telling' and exposes his deal with Lechero, questioning if he's the right man for the job. Hearing the Sona siren, Linc flees by car and when Susan calls, he lies, telling her he has the 'escapees' in the trunk, but Pike, another company operative phones her: the roll-count was complete. Sucre stops her van by crashing into it, but even when Linc holds her at gun-point her accomplice won't trade L.J. He releases her and gets a short extension to find out what happened. Failing a hearing, Malone now believes Justice official Richard Sullins is setting him up to confess. Michael is dragged before Lechero, but not to be punished, he's ordered to take the fallen boss along when he and Whistler escape. Susan asks instructions from Whistler, he tells her - as Gretchen - to give the brothers four more days.

Michael, Mahone, Sucre and Lincoln try to get into the house where Scylla is being kept safe. T-Bag and Sancho head to San Diego in the desert.

Sammy reminds Lechero that Papo is dead and presses Lechero to kill Michael. Lechero replies that he also wants Michael dead, but he does not want an uprising in Sona. Mahone receives a picture of his son through the mail. Lechero, Michael, Mahone, Whistler and T-Bag inspect the hole in the tunnel and Michael requests a saw and hammer to support the tunnel. Sammy takes the over the reign of Sona with the pistol delivered by Augusto and other three gangsters and promises a box of bottles of rum for the inmate that kills Michael. T-Bag convinces Bellick to give the chicken foot to Sammy, promising him a spot on the escape team. When Bellick discovers that there is no more acetone, he unsuccessfully tries to call-off the fight. Meanwhile Lincoln and Sofia visits Osberto and buy a bomb. Sucre plants the bomb under the seat of Gretchen's car but she unravels that, saying she found Maricruz tracking the US$ 25,000.00 check she gave to him. Sammy leaves the fighting with Bellick to chase Michael, who is locked behind the door in the tunnel with Mahone. Sammy beats Whistler, who was left behind, trying to get the combination of the door. Michael removes a wedge from the hole and the tunnel collapses over Sammy, burying him, while Lechero and Mahone kill the three other gangsters. Sofia finds a wallet hidden in Whistler's bag.

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.

A test with a rat proves the tower snipers are very good, so Michael figures the only option to breaking Whistler out within 24 hours has to be at 3 PM, during the distraction of soccer game. Sucre accepts $5,000 from Lechero's cousin, Augusto, to smuggle a package into Sona. Linc is to arrange transport outside, but he and Sofia get turned away roughly by an army patrol two miles away. He tells her Sara has already been killed. He keeps it from Michael, as LJ is his ultimate priority. New prisoner Andrew Tyge is robbed to his boxers on arrival, and recognizes Whistler (who denies it), mentioning the McFadden, Nice in 1997. He is warned off by Mahone who has noticed Tyge snooping around Michael and Whistler. They plan an electric signal disturbance device to distract the guard tower. Before they can make a move, a reflection from the binoculars is spotted: the troops move in and find it in his cell. Michael admits it's his. When the commander is about to shoot him, Whistler claims it's his for bird-watching, and proves it showing the ornithology book (the one Linc couldn't hold on to).