This season begins eight hours after the escape from prison; focusing mainly on the escapees. The fugitives split up and journey to locations across the country with the authorities close behind them as they each pursue their individual goals. Several of the escapees reunite in search of a large cache of money buried long ago by another prisoner. Federal agent Alexander Mahone (William Fichtner) is assigned to track down and capture the eight fugitives but is revealed to be working for The Company, which wants all eight men dead. All while the brothers try to bring down the current President, a Company member, to ensure the brothers' safety and avoid getting caught. Several of the escapees are killed or recaptured, but the brothers make it to Panama. Lincoln is exonerated, but Michael, T-Bag, Mahone, and Bellick are arrested by the Panamanian authorities and imprisoned at the Penitenciaría Federal de Sona.
