Veronica and Nick request a judge to postpone Lincoln's execution. A C.O. becomes suspicious about a broken door.

As Lincoln is about to be executed, he briefly sees his father in the viewing room. A phone call from judge Kessler delays the execution. After reviewing the newly surfaced evidence, the judge orders the exhumation of Steadman's body.

Michael creates a new, more dangerous, break-out plan, involving going through the prison yard. An accident puts Michael's new plan in danger.

As the escape is in progress, Warden Pope and Captain Bellick begin a search to detain the escapees. Michael and co. have to reach the aircraft fast as the police is hot on their heels. Veronica discovers a major piece of evidence that could prove Lincoln's innocence. The Vice President is worried about losing her authority.

As eight hours has passed since the escape, Michael, Lincoln, Sucre, C-Note and Abruzzi attempt to evade their seekers. Bellick is forced to relinquish the command of the search party to FBI Special Agent Alexander Mahone whose ingenious approach makes Michael's life as a fugitive harder. As a result from her overdose, Dr. Tancredi is in critical condition. A short-handed T-Bag faces the ultimate challenge.

In an effort to learn more about his pursuer Michael cozies up to Mahone's wife. L.J. and Lincoln have a bumpy road-trip. T-Bag receives a surprise, and C-Note's wife must choose between her daughter and husband.

Bellick gets a taste of the medicine he gave out when he was the Captain and Agent Mahone's ex-wife makes another appearance.

Michael tries to save his brother and himself from the unstoppable Mahone. Kellerman's testimony at Sara's trial proves different from what was expected, could this be the end for Sara? 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.

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.

Michael threatens to cancel the escape plan unless he sees a proof that Sara 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.

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 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 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.

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 tries to bring down the Company once and for all.