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.

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.

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.

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.

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.

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.

Despite Michael's condition, the team goes forward with their plans to steal Scylla. Gretchen and T-Bag work together to get the sixth card from the General but without success. Michael, Lincoln, Sucre and Mahone break through the wall.

Michael and the gang pull off the Scylla heist from deep within Company headquarters - but a terrible surprise awaits them.

As the gang deals with Don's betrayal, Lincoln is captured. Meanwhile, Don forces Gretchen to help him by holding her daughter and sister hostage.

Don and Gretchen, Michael and The Company are all after Scylla. Elsewhere, T-Bag has to make a tough decision as he holds Gretchen's family hostage.

When Michael undergoes surgery, he has visions of Westmoreland. Meanwhile, Lincoln and Sucre try to retrieve Scylla before Don and Gretchen sell it.

Lincoln calls Sara from Miami asking for news about Michael and tells that he is trying to retrieve the Scylla for The Company with Gretchen, T-Bag and Self. They find a lead in the Grafton Club, and Lincoln goes to the place where he abducts Tia Hayden trying to find the representative of the owner of Scylla. Meanwhile Michael awakes locked in a house in the woods under the surveillance of bodyguards of The Company. The psychiatrist, Dr. Roger Knowlton, tells him that his mother is alive and is working for 'The Company' in the Madagascar Rainforest. He wants to prepare Michael to join 'The Company' and use his skills on a global scale working with his mother. Tia lures Lincoln and manages to escape, but he keeps her wallet and finds her address. Sara tells General Krantz that she wants to stay with Michael, but he says no to her. T-Bag and Self go to Tia's house and Self plots against the Lincoln's leadership. They bring pictures and a HD they found in the house. Self argues with Lincoln and Mahone arrives to balance the situation. Michael sees pictures of his childhood and recalls his family reunion while Dr. Knowlton evaluates him for General Krantz and is pressed to use a quick and nasty process to force Michael to join The Company. Lincoln and Mahone go to the marina to investigate the representative of the owner of Scylla. Sara receives a mysterious cellphone message for a meeting and is abducted near a public phone by Lisa's men, and Lisa tells her that Michael is 60 miles northeastern downtown. Gretchen finds Scott, the representative of the owner of Scylla, while researching a database, but she lures the rest of the group and meets with Scott who promises ten million dollars for her. T-Bag overhears the conversation between Sara and Lincoln and calls General Krantz. He in turn orders Dr. Knowlton to drug Michael for transportation. However Michael reverts the situation and escapes running through the woods. Sara manages to rescue Michael. When the group meets Scott, there is a shootout and Gretchen is hit and left behind. In the end, the surprising owner of Scylla finally appears.

Lincoln and his men (Self, T-Bag, Mahone) are trying to find Scylla. They try to find a clue for the key from the fake buyer who killed Gretchen. They find a Church and an Estate that matches with key. When Lincoln and Mahone investigate the Estate, Lincoln finds a picture of him with his mother. Mahone finds out that, picture was edited and some clue about meeting place. Lincoln takes the meeting and finds his mother. Christina wants 2 days from Lincoln for eliminating Krantz. By the way Company's men finds Michael and Sara, they run away with truck and escape again. At last Lincoln goes to meeting place again and beginning of the end starts.

Michael and Lincoln square off over Scylla as Christina sets her plan in motion. Meanwhile, T-Bag causes a scene at the Indian embassy.

Michael has an uneasy reunion with Christina, who drops a bombshell regarding Lincoln. Elsewhere, Lincoln races to stop Christina's deadly plan.

Pandemonium erupts at the Panda Bay Hotel after an assassination at the global energy conference.

As familiar faces return to help Michael in his quest to bring down The Company, Lincoln makes a discovery about his relationship with Michael.

After the general catches the brothers and raises the stakes by abducting more of their relatives, Michael escapes with Scylla.

Michael and Sara's newfound happiness is short-lived, as Sara soon finds herself in prison, and Michael must break her out before a vengeful Krantz has her killed.

In a continued 90 minute episode, Michael and Sara's newfound happiness is short-lived, as Sara soon finds herself in prison, and Michael must break her out before a vengeful Krantz has her killed.