The third season of Prison Break is set in Panama and inside Sona, a prison run by inmates after riots broke out there, a year back. While Michael is now inside Sona, Lincoln is outside yet within Panama. Gretchen Morgan, a company operative in charge of the Panamanian operations, gets in touch with Burrows, whose son LJ was kidnapped by Gretchen. Michael’s love interest, Sara Tancredi also establishes contact with Burrows. The intention of the communication is to have James Whistler released from Sona.

The entire season revolves around Michael and Whistler’s attempts at escaping their respective entrapments. During the attempts, Michael has to deal effectively with all the stresses he’s been facing in his life while Lincoln has to deal smartly and effectively with Gretchen. In the interim, Sucre comes as a godsend for Michael’s plans to escape. Yet, when Lincoln tries to liberate Sara and LJ, using hints provided by Sara herself, his attempts are blighted by Gretchen’s assertion of having decapitated Sara, whose head he has sent to Lincoln as a forewarning.

Yet, by the end of the season, both Michael and Lincoln manage to break free along with Mahone and another inmate by the name, McGrady. Amidst all this, they leave numerous other inmates behind, including Bellick and T-Bag. Also, even after escaping, Sucre’s identity is caught by a prison guard, and so, put back into Sona. While Michael is thirsting for Gretchen’s blood – for Sara’s murder, LJ and Sofia manage to find themselves traded for Whistler, as it was Sofia who was incarcerated with the assurance that Whistler would accompany her.