Clues surface that suggest a previously thought-to-be-dead Michael may be alive. Lincoln and Sara, Michael’s wife until he was presumed dead, reunite to engineer the series’ biggest escape ever, as three of Fox River State Penitentiary’s most notorious escapees, Sucre, T-Bag and C-Note, are pulled back into the action.
As Lincoln and C-Note search for the “Sheik of Light,” Michael and his cellmate, Whip, attempt an escape from Ogygia. Meanwhile, Sara’s investigation into Michael’s reappearance leads her to the state department and an uneasy reunion with Paul Kellerman.
T-Bag ambushes Sara and warns her that two of Poseidon’s henchmen, Van Gogh and A&W, may be following her. Lincoln attempts to retrieve his confiscated passport to escape Yemen and Michael plans his next move
Michael, Whip and Ja make their last attempt to break from Ogygia, but must make a deal with the devil to do so. Lincoln races against the clock to help with the escape, as T-Bag meets with Kellerman to gather more info on Michael's resurrection.
Lincoln becomes frustrated as he tries to understand what really happened to Michael. C-Note has a new escape plan, but fears it will not be executed quickly enough, as Cyclops is trailing closely behind. Meanwhile, Sara struggles with the idea that Michael may be alive.
As Michael, Lincoln and the remaining Ogygia gang try to escape Yemen, they find themselves racing though the desert from a vengeful Cyclops. Meanwhile, A&W and Van Gogh question their roles as their pursuit of the escapees leads them to...Graceland.
Sara becomes fearful of her family's safety when she discovers the real reason that Michael faked his own death. In the meantime, Michael and Lincoln continue to try find a way home with the help of Sucre, and the real identity of Poseidon is revealed.
When Sara and her son are threatened, Michael and Lincoln recruit the help of Sheba and C-Note to catch Poseidon; Whip sets out on a separate mission; T-Bag reveals a secret.
Everything goes wrong for Michael as he tries to create a diversion. Lincoln tries to outsmart Susan who has his son. Sucre offers his assistance to Lincoln.
Susan jeopardizes Michael's life as she puts her own escape plan into motion. Whistler's past catches up to his girlfriend.The Company goes after Lincoln and Sucre. Justice prevails for Mahone. And Lechero sheds light into an empty tunnel.
The Panamanian Army arranges Michael to get a taste of solitary. T-Bag reserves a spot in the escape. Bellick's life turns into an uphill battle. Susan traps Sucre.
Lechero's demotion devastates Michael's breakout plan as Sammy takes reigns at Sona. T-Bag forces Bellick to fight in a fight where the odds are stacked heavily against him. Lincoln and Sucre have some surprise fireworks set for Susan.
Michael's escape may be in jeopardy because of heavy rain. T-Bag and Lechero join forces, while Bellick hopes to do the same with Mahone.
Michael, Whistler, and Mahone make their break from Sona. But Mahone seems like the odd man out along the way.
Michael and Lincoln are left with no choice but to hand Whistler over in exchange to save LJ and Sofia. A familiar face enters Sona while another inmate leaves.
Michael threatens to cancel the escape plan unless he sees a proof that Sarah is still alive. Whistler is accused of murdering an inmate and it is up to Michael to prove his innocence and save his life. Lincoln and Sofia help in monitoring the morning guards. Mahone may have another way to get out of Sona.
A new inmate named Tyge is brought to Sona. After he seemingly recognizes Whistler, Michael's doubts arise. T-Bag enters a new area of commerce.Lincoln goes to the seaside with Sofia. Sucre takes over the side-business of his predecessor.
Now locked up in a Panamanian prison known as Sona, Michael, T-Bag, Bellick, and Mahone try to find a way out. Much to their devastation, they soon find out that the prison has been abandoned by the authorities because of the immense threat from the vile inmates. Michael seeks for an inmate named Whistler in the prison sewers. As Lincoln is puzzled by Sara's sudden disappearance, he learns that LJ has gotten into some trouble. He also tries to recover the 5 million dollars.
After taking delivery of a package from The Company, Lincoln realizes that they are deadly serious. Michael's new break out plan relies on electricity. Haywire is back from the dead, haunting disoriented Mahone. Bellick and T-Bag get special attention from Lechero.
Whistler tells the truth to Michael. Michael tries to get in touch with Sara but the only phone is in Lechero's quarters, so he has to rely on T-Bag's help. Mahone battles his addiction. Bellick steps on some toes.
Michael has trailed Gretchen/Susan, Whistler and Mahone to L.A. Chaos reigns in SONA while T-Bag, Bellick and Sucre go missing. Lincoln and L.J. continue to stay with Sofia.
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 attempts to track the cardholder and avoid going back to prison. Wyatt finds new information regarding Sara's whereabouts. Elsewhere, T-Bag uses a new identity to make a new life for himself.
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.
Self locates another card hidden in a safe within a secure federal building, as Mahone continues his quest for revenge. Meanwhile, T-Bag's new life may be in jeopardy.
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.
Sara is left with no choice but to take Michael to the hospital as his condtion rapidly worsens. Sucre and Lincoln are faced with unknown territory as they are left in charge of the operation. Elsewhere, agent Self makes a surprising ally.
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.
Sara takes a hostage in a bid to secure Scylla. In the meantime, Michael and Lincoln finally meet the General while one of their members switches allegiance.
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.
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 Sara journey to Miami while Lincoln meets with his mother. T-Bag and Self's mission to locate Scylla takes a dramatic turn. The General comes under pressure.
Michael and Lincoln come to blows over Scylla as Christina sets the wheels in motion for her plan. Meanwhile, Sara receives life-changing news. T-Bag arrives at the Indian Embassy. The General becomes increasingly paranoid.
Michael's reunion with Christina is soured when she drops a bombshell regarding Lincoln, and T-Bag grows determined to prove he is worthy of being a member of the Company.
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.
Michael tries to save his brother and himself from the unstoppable Mahone. Kellerman's testimony at Sarah's trial proves different from what was expected, could this be the end for Sarah? Sucre puts everything on the line to save his Maricruz. Just like old times, T-Bag and Bellick are at it again but this time there will be a winner.
The day has finally come for Sara's trial while critical information that will exonerate her is being debunked. Meanwhile, Michael is determined to get his hands on the 5 million and to stop T-Bag's reign of terror. Bellick is also money hungry and will do whatever it takes to hunt down T-Bag. Kellerman decides his fate while Lincoln and Mahone square off.
Sara sacrifices herself for the safety of Michael so the brothers can get on with their final plan to attain freedom, but their plan gets 'shipwrecked'. Meanwhile, Bellick blackmails Sucre to partner up as T-Bag's streak of murder continues to the south of the border.