In the season two of the series the prisoner from Fox River State Penitentiary escaped including Scofield and Lincoln. New characters are introduced including federal agent Alexander Mahone, who is assigned to track down and capture the eight escapees. The fugitives journey to locations across America with the authorities close behind them as they each pursue their individual goals. The Company continues their plan to locate and eliminate Lincoln Burrows and others who get in their way. As the season progress many conflict emerge regarding the case of the fugitive, until the President step down to protect herself and the nation from the thing she did. It is because Scofield made an agreement to the President that in exchange of their freedom which is need to be done in the President SONA is the tape revealing the President adultery. However the President made her decision and the only choice that the brothers can do is to disappear forever. The Next step is to go to Panama where it is planed before by Scofield. The plot continue where most of the main characters have ended up in Panama.
In season three the plot continue from the second season finale, it is much different in tone from the previous seasons. Lincoln is exonerated from his alleged crimes and Michael is imprisoned at Sona Federal Prison facing a homicide charge. In these season some of our characters has their redeeming moments and Michael soon discovers that he was purposely placed in Sona to engineer another daring and seemingly impossible prison break. This is to free Whistler, a mysterious inmate hiding within the prison’s sewer system. Lincoln must work outside the prison walls to help the plan of escape, as well as rescue his kidnapped son, LJ, and Michael’s true love, Sara Tancredi.