Sara has been jailed for murder. Wanting to make an example of her, the government has sent her to a women's prison and she faces 25 years to life. Heavily pregnant and fearful for her life, Sara must survive by making an alliance with an old enemy... but she's a marked woman and various attempts on her life lead Michael to take drastic action.

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

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

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.

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.

Michael and Lincoln square-off over Scylla as Christina orders a kill shot and set sets her plan in motion. Sara receives some unexpected news, T-Bag causes a scene at the Indian Embassy and Pad Man's paranoia leads to a death.

Michael and Sara 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.

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 info about his past. Meanwhile, a double-crossing leads to a death and an arrest.

Michael gets medical attention from the most unlikely of places, and Charles Westmoreland returns to help uncover the true meaning of Scylla. Meanwhile, Lincoln and Sucre race to stop Gretchen before Scylla is lost forever.

Michael and Lincoln race to get Scylla back from Gretchen and her new partner who are just as determined to get a missing piece of the puzzle from the brothers. Meanwhile, Mahone meets with an old colleague who is torn between friendship and duty, and T-Bag's faith is put to the test while holding Gretchen's family hostage.

Michael must hold the team together after they are betrayed by one of their own. T-Bag gets a new partner who blackmails Gretchen into finding a buyer for Scylla.

The search for Scylla comes to a shocking end as Sara takes a hostage, T-Bag and Gretchen have their last stand at Gate, and Michael and Lincoln come face-to-face with the General and are betrayed by one of their own.

Michael races against time and his ailing health to break into the Company headquarters to steal Scylla, but the break-in's success lies with Sucre. Gretchen dresses up for a meeting with the General and one final attempt to get the last card key. T-Bag must make a decision to leave his criminal ways for good.

Michael's medical condition forces Sara to take him to the hospital, and Sucre and Lincoln get themselves into an explosive situation. Mahone has designs on the Company's architect while Agent Self meets with a surprising ally.

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.

Lincoln and Sucre target Pad Man to obtain the sixth and final card key, and Gretchen gives Sara an opportunity to settle the score. Michael and Roland each make deals with different devils, while a team member finds himself on the wrong end of a bullet.

Lincoln takes members of the team to Las Vegas where Sucre gets an indecent proposal. Sara 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.

Michael and the gang track a key card holder to a racetrack while Mahone gets caught with something invaluable. Gretchen has a family reunion, and Self lands on Wyatt's radar. T-Bag begins to unravel Whistler's code.

The search for the next card key holder brings Michael and Lincoln to the Treasury Department. Sucre and Bellick track T-Bag, who arouses suspicions and forms an uneasy alliance at his new job. Wyatt uses his personal touch with Gretchen.

Michael, Lincoln and Sucre must crash a police benefit to obtain the next card key. Reeling from another death, Sara falls back into an old habit. T-Bag arouses suspicion and runs into some old "friends" his first day on the job.

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 the others get a new team member, Roland, and work to copy the data card. Wyatt continues his quest to find the brothers. T-Bag makes his way north.

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.