- S3 E1 - OrientacionThe season opener finds Michael Scofield in Sona, a hellish and deadly Panamanian prison where a previous riot has forced all authority out and has left the prisoners in charge of their own lives (and deaths).
- S3 E2 - Fire / WaterMichael races to find a hidden Whistler before Mahone; searching for clues outside the prison, Lincoln runs into an old friend and makes a new one; T-Bag slithers his way into Lechero's graces as the prisoners threaten a revolt due to the lack of agua (water).
- S3 E3 - Call WaitingDetermined to speak with Sara, Michael enlists T-Bag's help to get to the only phone in Sona: Lechero's; Lincoln attempts a daring rescue; Whistler comes clean to Michael, just as Mahone is tempted to fall back on a dirty habit; and Bellick makes an enemy while attempting to get back on his feet.
- S3 E4 - Good FencesAfter his failed attempt to rescue LJ and Sara, Lincoln receives a deadly warning from The Company; Michael formulates an electrifying escape plan from Sona; Mahone is haunted by a face from the past; and T-Bag crawls up the ladder as Bellick lands in hot water with Lechero.
- S3 E5 - InterferenceA new inmate enters Sona, unnerving Whistler and raising Michael's suspicions.
- S3 E6 - Photo FinishWhen an inmate is found murdered, Whistler becomes the prime suspect and Michael must prove his innocence in order to save his life.
- S3 E7 - VamonosMichael demands evidence from Susan that Sarah is alive, or he will cancel the escape.
- S3 E8 - Bang & BurnSusan takes the escape into her own hands, leaving Michael's life hanging in the balance; Lechero reveals a secret buried beneath Sona; Sofia uncovers more of Whistler's past; Mahone's freedom hinges on his testimony; and Lincoln and Sucre are targeted by The Company.
- S3 E9 - Boxed InAfter raising the suspicions of the Panamanian Army, Michael sweats out solitary Sona-style while Bellick weathers the fight of his life.
- S3 E10 - Dirt NapWhen Lechero loses his authority over Sona, Sammy causes Michael's escape plan to come crashing down.
- S3 E11 - Under & OutHeavy rains force Michael to move up the escape timetable and break out of Sona that evening.
- S3 E12 - Hell or High WaterMichael and his fellow inmates make their break from Sona, but the escape doesn't go as planned for all of them.
- S3 E13 - The Art of the DealMichael & Lincoln must handover Whistler to Susan so they can save LJ and Sofia's lives;.
- Content advisory
- Violence substance use alcohol use smoking foul language sexual content
- None available
- Bobby RothKevin HooksDwight H. LittleNelson McCormickKaren GaviolaMichael SwitzerGuy FerlandGreg YaitanesVincent MisianoMilan Cheylov