Original channel: FOX
Country of origin: United States
Original present: 2007
Format: Drama, Thriller, Action
Created by Paul Scheuring
Language: English

Season 3 follows both Michael inside Sona and Lincoln on the outside in Panama. Sona is a prison that has been run by the inmates and guarded only from the outside since a riot the year before. Burrows is quickly contacted by The Company who have kidnapped his son LJ (Marshall Allman) and Sara Tancredi (Sarah Wayne Callies), the woman Michael loves. He is told that they want Scofield to break James Whistler (Chris Vance) out of Sona. The season follows Michael and Whistler's trials in formulating an escape plan, as Michael has to deal with extreme tension and as Lincoln deals with the Company's operative Gretchen Morgan (Jodi Lyn O'Keefe). Sucre gets a job at the prison to aid Michael in his escape plan.

When Lincoln attempts to rescue Sara and LJ following a clue provided by Sara, Morgan "beheads Sara" and sends Lincoln a head in a box as a warning. As the season ends, the pair manage to escape along with Mahone leaving behind several accomplices including T-Bag and Bellick. Sucre's identity is discovered by a prison guard and is thrown into Sona just after the escape. LJ is traded for Whistler, and Michael is out for revenge against Gretchen for "Sara's death".