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.

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.

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.

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.

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, 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.

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.