Lincoln is sentenced to death and is incarcerated in Fox River State Penitentiary where he awaits his execution.
Lincoln's brother, brilliant structural engineer Michael Scofield, is convinced of Lincoln's innocence and formulates an escape plan.
The Company was responsible for framing Lincoln, and they did so because of Lincoln's father Aldo Burrows, and his former connections with The Company.
The brothers, along with six other inmates, Fernando Sucre, Theodore "T-Bag" Bagwell, Benjamin Miles "C-Note" Franklin, David "Tweener" Apolskis, John Abruzzi, and Charles "Haywire" Patoshik, who come to be known as the Fox River Eight, escape in the episode immediately prior to the season finale, after using their prison industry privileges to dig an escape tunnel underneath the prison.
The second season begins eight hours after the escape, focusing mainly on the eight escapees.
Series creator Paul Scheuring describes the second season as "The Fugitive times eight" and likens it to the "second half of The Great Escape." The fugitives split up and journey to locations across the country with the authorities close behind them as they each pursue their individual goals.
Two additional episodes, titled "The Old Ball and Chain" and "Free" were produced, and were later transformed into a standalone feature, titled The Final Break.
The events of this feature take place before the last scene of the series finale, and are intended to conclude unfinished plotlines.
Several of the escapees reunite in search of a large cache of money buried long ago by another Fox River inmate, Charles Westmoreland.
In order to gain access to Fox River, Michael commits an armed robbery which results in him being sentenced to Fox River.
In prison, Michael befriends the prison doctor Sara Tancredi when he pretends to suffer from Type 1 diabetes, in order to gain daily access to the prison's infirmary, when he receives his daily insulin shots.
The series has spawned an official magazine and a tie-in novel.
The fourth season of Prison Break returned from its mid-season break in a new timeslot on April 17, 2009, for the series' last six episodes.