Burrows is quickly contacted by The Company who have kidnapped his son [[L. J. Burrows|LJ]] ([[Marshall Allman]]) and [[Sara Tancredi]] ([[Sarah Wayne Callies]]), the woman Michael loves, and is told that they want Scofield to break [[James Whistler (Prison Break character)|James Whistler]] ([[Chris Vance (actor)|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 Michael fails to meet their deadline and Lincoln attempts a double-cross, Morgan "beheads Sara" and sends Lincoln the head 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".
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Prison Break sæson 3 består af 13 afsnit efter at være klippet ned fra 22 afsnit som følge af [[Writers Guild of America]]s [[strejke]] under vinteren 2007/2008. Afsnittene blev i USA sendt fra d. 17. september 2007 til d. 18 februar 2008 på Fox Networks.
