Following the explosive events of the Season 2 finale in Panama, Michael Scofield (Wentworth Miller) is incarcerated in the Penitenciaría de Sona (Sona Federal Prison). Unlike Fox River, Sona is run entirely from the inside by the inmates due to a violent riot that drove out the prison guards a year prior. The Panamanian military only guards the perimeter, leaving a brutal internal hierarchy to govern the prisoners.

Michael begins mapping out his escape route but realizes he needs more electrical power. Meanwhile, Mahone (William Fichtner) begins suffering from severe withdrawal symptoms. Episode 5: "Interference"

Michael adjusts to the lawless brutality of Sona. Mahone suffers from withdrawal, while Bellick is stripped to his underwear at the bottom of the food chain. Episode 2: "Fire/Water"