The gang has to break into the well-guarded home of company man Stuart Tuxhorn. Elsewhere, T-Bag must go to extremes to survive. S4, Ep3. 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.
S4, Ep4. 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. S4, Ep5. 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. S4, Ep6. Mahone is arrested, putting the whole gang at risk - and Mahone squarely in Wyatt's sights. Meanwhile T-Bag's charade is discovered. S4, Ep7. Lincoln, Sucre, Sara and Roland follow a Scylla cardholder to Las Vegas, where Roland has his device commandeered after he gets caught gambling. S4, Ep8. 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.
S4, Ep9. The team needs to make their way through a 30,gallon water main to get to Scylla. Meanwhile, T-Bag fends off an investigation. S4, Ep 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.
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. 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 Bagwell kills his friend and eats him in order to survive.
He is given a ride by bikers to San Diego, mentioned in the book, where he recovers important material from a box.
The team finds out that they only have one of the six cards that form the complete Scylla. Scofield notices his nose bleeding. The team investigates other data recovered from the mansion in order to find the other cardholders. Mahone asks FBI agent Lang to help him find his son's killer. Self's supervisor, agent Herb Stanton, convinces Senator Dallow to order the abort of the mission.
The team recovers emails, which are incomplete and they infiltrate the server building and obtain the rest. They manage to find the meeting location and Scofield proceeds while the others are arrested too.
Scofield returns with a film he recorded showing the faces of the six cardholders, one being the General himself. Self decides to let the team continue the mission.
Meanwhile, Mathewson gets no information from Bennett and kills him. Bagwell begins having fun in Whistler's house and calls a company called 'GATE' and is requested to go and receive his check. Mahone receives a file from Lang containing the possible shooters.
The team discovers that his son is killed and Burrows finally reconciles with him. The team believes the Turkish consul is a cardholder, but realizes that his wife, Lisa Tabak who is also the General's daughter, is. They find her difficult to get close to before spotting Bagwell and capturing him; but they can't find the book and he escapes.
The team finds out that Tabak will attend a police celebration. Scofield, Burrows and Mahone wear uniforms and successfully copy the card; but one of her bodyguards recognizes and follows Burrows and the latter kills him by Bellick's help. Meanwhile, Tancredi is informed of Bennett's death and gets depressed. She goes to a pub, where a man steals and uses her credit card, which is detected by the Company. The former notices a name, Xing, in the book.
Mahone instructs Glenn to help him find his son's killer. Mathewson arrives at the pub and starts chasing Tancredi. Mahone's wife, Pam, identifies Mathewson and encourages him to kill the latter. Tancredi manages to lose the latter and the team realizes that he wants to kill them. They move for the next card while Mahone starts investigating Mathewson.
Self enters the cardholder's room and fails to copy the card, but gives the specifics of the safe to the team and gets them in the building. Burrows notices Scofield's nose bleeding. They manage to copy the card while Oren, the cardholder, is meeting the General, who states that Scylla is the reason the Company has power.
Meanwhile, Mahone finds the motel Mathewson was staying in and notices the acceptant calling Mathewson, and takes the number by force. Morgan manages to free herself. Sucre and Bellick search the nearby buildings for Bagwell and tell Smith that there is a prize for helping them find Bagwell; but she decides to get more from Bagwell instead.
Bagwell is visited by Feng Huan, Xing's boss, who threatens to kill him if he doesn't get Scylla soon. The team deduces that the General is the head of the Company. The team manages to copy the next card with an elaborate plan; but Mahone is arrested by the police while recovering Glenn's device; and Self only manages to get the device. The team is divided whether to save Mahone or move to the next card. They finally choose to rescue him in the court, where Mathewson has also arrived to kill him.
Mahone is saved successfully. He calls Mathewson and promises to find him before throwing the number away, which is recovered by Glenn. Meanwhile, Gretchen reunites with her sister, Rita, and daughter, Emily, who believes Rita is her mother.
Gretchen recovers a gun and some money from a gift she had given Rita previously and proceeds with plans of working for herself. The General has found out Self's investigation on him and orders a DHS double agent to search his computer and Mathewson to warn him. Blauner finds illegal background in Bagwell's faked career and the latter clears the house and attempts to escape before being attacked by Gretchen. Bagwell offers Morgan to work together. Mahone advises Self to take the fight to the General instead of hiding; and Self makes the latter cancel the assault on him.
The team realizes that Scuderi, the next cardholder, is currently in Las Vegas, while they are informed by Smith of Bagwell's whereabouts. Scofield, Mahone and Bellick stay to find Bagwell while the others travel to Vegas. Burrows tells Tancredi of Scofield's condition, which resembles to what killed their mother at that age. The card is successfully copied; but Glenn's indiscretion results in losing the device. Meanwhile, Scofield's team realizes that the call was a ruse by Bagwell; only Mahone manages to escape.
Bagwell forces Scofield to reassemble the blueprint hidden in the papers of the book. Mahone finds the house by the GPS devices; but they are already gone as Morgan spotted the devices in time.
Morgan kills Blauner as a caution. Mahone arrives and Bagwell is locked in a room. Scofield gets a call from Morgan, who hid herself the whole time. Morgan makes a truce with Scofield, giving him the rest of the papers and Bagwell is released. They decide to work together to bring down the Company. Burrows suggests an attack on Krantz' car and taking the last card, which is approved. Glenn is cast out of the plan because of his indiscretion that resulted in losing the device.
He offers the team's whereabouts to Mathewson in exchange for money and proves his validity by giving the team's plan away, resulting in Sucre being critically shot, whose wounds Tancredi tends to. Glenn goes to meet Mathewson, who shoots and tortures him to tell the team's location. Having followed Glenn by a tracker Scofield put in his laptop, the team arrives and abducts Mathewson, everyone apart from Michael leaves Glenn to succumb to his wounds.
Meanwhile, Feng tries to kill Bagwell as he promised; but Morgan convinces him to give them more time. Bagwell instructs Smith to investigate the others. Tancredi reconciles with Morgan because of the team. Deducing that the attempt was for his card not his life, Krantz decides to transfer Scylla.
The team tortures Mathewson to make him tell Krantz that they are dead while preventing Mahone from taking his revenge until the deed is done. Tancredi is chosen to convince Mathewson; but she fails. It is revealed to be a plan to record his voice using different words and Self assembles those words, making a sentence stating the mission's accomplishment, which Self plays to Krantz on the phone; and he gets relieved and cancels the newspaper coverage he planned.
Mahone tortures Mathewson until he agrees to express apology to Pam, after which he is killed. Meanwhile, White starts investigating Blauner's disappearance; but Bagwell solves the situation by manipulating the records, showing the illegal background in Blauner's career, making White to close the case in order to prevent the scandal.
Morgan apparently reconciles with Krantz, revealed to have been involved with him before. She finds out about the transfer. The team finds a water pipe blocking their way and manages to get across it, but at the cost of Bellick's life. The team forces Self to recover Bellick's body and send it to his mother.
Sucre reveals that he would have died in the Sona riot, incited by Bagwell, if Bellick hadn't saved the former. Morgan informs the team of Krantz' plan. They realize that they can't translate the blueprint without the legend. They find an architect's name in the papers; and Mahone goes to the architect's house, where Krantz has sent his own men to recover the architect for his plan. The team finds mines in a room they reach on their way. Sucre puts his foot on a mine, which will detonate after the foot is pulled.
Morgan tries to defuse it. Mahone recovers the legend and manages to defuse the mine and save Sucre. Bagwell realizes that Smith is knowing more than expected. He gets her call register and finds out that she is in contact with Self. Meanwhile, Scofield is diagnosed with hypothalamus hamartoma and Tancredi states that he will die if he doesn't have a surgery soon.
Scofield designates the plan for the team, as he will not join them because of his surgery. Morgan arranges a tryst with Krantz, in which she tries to steal his card; but he already knows and tries to kill her before she reminds him of their child; and he spares her and leaves.
Scofield decides to join the team and finish the mission before surgery; and Tancredi goes to do her part, revealed to be involving Tabak. Morgan and Bagwell prepare to kill Scofield's team when they come back with Scylla. Smith intercepts Bagwell's call about a buyer and teams up with Self to enter the house, where Feng's men capture them. Scofield's team starts working silently because of the sound sensors. They get past the wall and make a ladder to reach the glass room while using nitrogen gas to avoid the temperature sensors.
They finally enter the glass room, which contains a box. As Scofield touches it, Krantz finds out and takes a team to neutralize the threat. The team takes Krantz hostage and uses the six cards to open the box and recover Scylla. They proceed to Krantz' room, where, he tries to allure them to surrender, reveling that he and Aldo Burrows worked closely. He finds out that Tancredi has taken Tabak hostage; and she will kill her if the team isn't allowed a safe passage outside.
The team leaves the building with Scylla and Krantz orders their chase. Meanwhile, Self and Smith manage to free themselves and kill Feng and his men. Smith arrives and saves them. The team separates, with the brothers taking the bag to an airport, where the Company operatives take it. But it is revealed that Mahone and Sucre actually have Scylla. The team gives Scylla to Self, who gives them a package containing their transfer papers and tells them to wait for the authorities.
They wait for hours without anyone coming and find out that the package contains plain papers. Self kills Hultz and takes Scylla. Self makes Stanton believe that the team has killed him and seized Scylla. The team deduces Self's plan, to sell Scylla and disappear.
They unite with Gretchen to find Self, who unites with Bagwell and they take Rita and Emily hostage, forcing Gretchen to give the team away to DHS and find a new buyer. The team is attacked by DHS agents and Burrows is captured.
Burrows manages to convince Stanton and Dallow of the truth. They offer a new deal for the team to testify against Self. Scofield instructs Mahone to get Tancredi and Sucre outside the city and proceeds to the warehouse to testify with Burrows. Stanton and Dallow decide to kill the brothers to prevent the scandal. The Company mole kills Stanton and other agents before Sucre arrives and saves them, with the mole being killed.
They let Dallow leave. Meanwhile, Krantz kills Scuderi for humiliating him. Bagwell stays at Rita's while Gretchen and Self meet a conduit, who reveals that a piece of Scylla is missing. Self calls Scofield and demands it, who defies him to come and get it. The team prepares for Self's attack.
They capture Self, who convinces them to let him sell Scylla and the Company will be destroyed anyway. They let him leave, while Sucre hides in his trunk. Self and Gretchen arrive in a motel and Sucre informs the others, who arrive and attack the duo. Scofield's condition makes him collapse; and the duo escape.
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