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.
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 information on Sara's whereabouts, while T-Bag finds the gateway to his new identity and future.
Michael, Lincoln and Sucre crash a police benefit in order to get the next card key. Tormented by another death, Sarah picks up an old habit. T-Bag causes some suspicion and runs into old "friends" his first day on the job.
Searching for the next card key holder leads Michael and Lincoln to the Treasury Department. Sucre and Bellick search for T-Bag, who arouses suspicions and forms an uneasy alliance at his new job. Meanwhile, Wyatt uses a personal touch with Gretchen.
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.
Lincoln takes the team to Las Vegas where Sucre gets a proposal. Sarah learns about Michael's condition, and Gretchen teams up with T-Bag who makes Michael an offer he cannot refuse. Meanwhile, the secrets in Whistler's bird book are finally revealed.
Lincoln and Sucre target Pad Man to get the final card key, while Gretchen gives Sarah an opportunity to even the score. Michael and Roland each make different deals, while a team member finds himself in some hot water.
Wyatt gets in to some trouble, and Mahone finds resolution. T-Bag runs when the police investigate his missing co-worker, while Gretchen warms-up to a Company man. Michael's condition worsens, and a team member makes a sacrifice while planning the break-in for Scylla.
Michael's condition forces Sara to take him to the hospital. Sucre and Lincoln get themselves into a situation, Mahone has designs on the company's architect, and Agent Self meets with an ally.
Michael races to break into the Company headquarters to steal Scylla, but the break-in's success depends on Sucre. Gretchen has a meeting with the General and a final attempt at getting the last card key. And finally, T-Bag must decide to leave his criminal ways for good.
The search for Scylla comes to an end when Sara takes a hostage. T-Bag and Gretchen have their last stand at Gate, and Michael and Lincoln meet the General and are betrayed by a member of their group.
Michael holds the team together after one of their own turns against them. T-Bag's new partner blackmails Gretchen to aid their search in finding a buyer for Scylla.
Michael and Lincoln get Scylla back from Gretchen and her new partner who also want the missing piece of the puzzle from the brothers. Meanwhile, Mahone runs into a colleague who is torn between friendship and duty, and T-Bag's faith is put to the test.
Michael gets medical attention in some unlikely places, and Charles Westmoreland comes back to help uncover the meaning of Scylla. Meanwhile, Lincoln and Sucre rush to stop Gretchen before Scylla is lost.
Lincoln and his partners arrive in Miami to take back Scylla from its new owner, and Sara searches for Michael who learns that his mother is still alive and working for the Company. Sara gets the address where Michael's being held and saves him after he escapes on his own. Meanwhile, Gretchen betrays the group which leads to the death of Scylla's buyer and a bullet to the chest.
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 a new enemy, and T-Bag and Self's search for Scylla leads to an unexpected discovery.
Michael and Lincoln square-off over Scylla as Christina orders a kill shot and sets her plan in motion. Sarah receives some unexpected news, T-Bag causes a scene at the Indian Embassy and Pad Man's paranoia leads to a death.
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.
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.
Familiar faces return to help Michael with his last shot at getting Scylla in the proper hands and dismantling The Company once and for all.
Familiar faces return to help Michael with his last shot at getting Scylla in the proper hands and dismantling The Company once and for all. Michael ponders fatherhood, and the story continues 4 years later.