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, Lincoln, Sara and the team work with Roland, a new team meber, to get a copy of the data card. Meanwhile, Wyatt continues his mission to track down the brothers while T-Bag makes his way north using the bird book as his guide.
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 Sucre must crash a police benefit to obtain the next card key. Reeling from another death, Sarah falls back into an old habit. T-Bag arouses suspicion and runs into some old "friends" his first day on the job.
Michael and Lincoln make their way to the Treasury Department in search of the next key card holder; an awkward alliance formed by T-Bag at his new job arouses the suspicions of Sucre and Bellick; Wyatt uses his magic touch on Gretchen.
The entire operation may be in jeopardy when Mahone gets into trouble with the law. Gretchen's sister receives a surprise visitor. The Company may be onto Self. T-Bag continues to raise suspicions at Gate.
Lincoln takes members of the team to Las Vegas where Sucre gets an indecent proposal. Sarah 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.
Lincoln works to retrieve the final card, which is being held by the General. Michael and Self are forced to work with Gretchen. Meanwhile, Roland continues to be berated for losing the transcribing device in Las Vegas.
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.
Meanwhile, Michael's condition continues to worsen, and a team member makes the ultimate sacrifice while planning the underground break-in for Scylla.
When Michael's condition begins to worsen, Sara has no choice but to take him to the emergency room. Later, Sara receives a shocking call about Michael's ailment. Meanwhile, Sucre and Lincoln find themselves in explosive territory; Agent Self makes a surprising ally; and Mahone is able to track down vital information about Scylla.
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.
As the search for Scylla comes to a surprising end, Sarah takes a hostage, T-Bag and Gretchen have their last stand at Gate, and Michael and Lincoln are betrayed by one of their own as they finally get to go face-to-face with the General.
It's up to Michael to hold the gang together after they find out they were betrayed by one of their own. Meanwhile, Gretchen is blackmailed by T-Bag's new partner.
Michael, whose condition is deteriorating, winds up in the hands of The Company who promise Lincoln that they can save Michael's life in exchange for a favor.
Elsewhere, Gretchen and Self wind up with Scylla and a buyer.
Michael recieves medical attention. Charles Westmoreland helps uncover the real secrets of Scylla. Lincoln and Sucre do everything in their power to retrieve Scylla before it's gone forever.
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 information about his past. Meanwhile, a double-crossing leads to a death and an arrest in "The Sunshine State".
Michael and Sarah 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.
Michael and Lincoln square-off over Scylla as Christina orders a hug shot and set 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 end his quest to bring down The Company once and for all.
According to Michael's plan, Mahone hands a fake Scylla to Christina. It's booby-trapped but ends up in the hands of FBI Agent, Chris Franco. Bagwell meets Sucre and C-note, but is caught while they hope that an offer of help is real. The General catches the brothers and raises the stakes with more kidnapped relatives. Michael manages to escape with Scylla. The gang must decide whether to believe an offer from Paul Kellerman, and hand it to UN representatives in exchange for full pardons.
Sara has been jailed for hug. 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.