Fox River State Penitentiary assumes many characteristics of its real-life counterpart, Joliet Prison. Its structure and layout are the same, with the exception of its three-tiered A-wing in contrast to the two tiers in Joliet Prison.
As shown in the episodes "Riots, Drills and the Devil (Part one and two)", the general prison population is divided into east and west cell blocks in A and B wings respectively. These two wings are completely segregated by the South wing, which holds the administration staff. In a subsequent episode, "The Old Head", it is revealed that the infirmary is located on the opposite end of the prison to the A wing. A storage room, which later became the correctional officers' break room, is located at the center of the prison, directly above the underground pipes.
Built in 1907, the prison has an extensive underground pipe system. In the episode "By the Skin and the Teeth", Michael Scofield (Wentworth Miller) explains to his cellmate, Fernando Sucre (Amaury Nolasco) that over the century the original lead pipes were replaced by copper pipes and then later, by industrial plastic pipes. The replacement pipes were laid over the older ones, making a complex network of pipes beneath the prison.
Days before the race riot, the tension between white and black inmates rose as they both prepared discreetly for the inevitable fight. The white supremacists led by T-Bag (Robert Knepper), a member of the Alliance for Purity, gathered weapons including shanks and a screw which Michael had loosened from the bleachers that had been claimed by T-Bag. The fight broke out during a head count which resulted in many injuries and deaths. The riot was stopped when the guards eventually regained control and Warden Pope initiated a lockdown for the following 48 hours.
Soon after, due to the schedule of escape plan, Michael was forced to shut off the air conditioner on the "hottest day in April in order to cause chaos among the other inmates and in so doing, forcing the guards to put the A-wing in lockdown. T-Bag continuously complained about the heat and eventually caused C.O. Geary (Matt DeCaro) to toss his drink in his face and initiated a lockdown. However, T-Bag and his followers refused to return to their cells, resulting in the guards retreating back behind the gates. The inmates then started pulling on the bars and later, gained access to the control room which allowed them to free the other prisoners, causing a full-scale riot. The riot was stopped after the Governor of Illinois, Frank Tancredi (John Heard) intervened and sent special units to regain control of the facility.
After Michael's brother, Lincoln Burrows (Dominic Purcell) was framed for the murder of Terrence Steadman, brother of then-Vice President Caroline Reynolds (Patricia Wettig), he was convicted and placed on death row at Fox River. Michael eventually developed an elaborate plan to break his brother out of prison. He committed an armed robbery, then allowed himself to be arrested, pleading no contest to the charges but requesting incarceration at a facility close by - Fox River State Penitentiary. Prior to his arrest, Michael had extensive tattoo work done over his upper body which included the plans for the prison and various other codes (hidden in the artwork, so as not to arouse suspicion). Once inside, he enlisted the aid of several inmates who would prove useful to the escape.
Though the escape attempt suffered a number of setbacks and a number of other inmates forced their way into the escape plan, they eventually successfully escaped climbing across a wire and going over the prison walls. Michael, Lincoln, and the six other escapees would come to be known as "The Fox River Eight" in the second season. They consisted of the following inmates:
Additionally, two other inmates, Charles Westmoreland (Muse Watson) and Manche Sanchez (Joseph Nunez) were involved in the escape plan, though Sanchez was captured, and Westmoreland died of injuries sustained earlier.
The Fox River Eight escape was the first successful escape in the history of Fox River State Penitentiary.
The escape of eight felons led to the dismissal of Captain Brad Bellick (Wade Williams) and the resignation of Warden Henry Pope. Dr. Sara Tancredi (Sarah Wayne Callies) was arrested and faced possible charges in aiding the escape, though she was later bailed out by her father, Governor Frank Tancredi.
Pope was succeeded as Warden of Fox River soon after by Ed Pavelka, a much more hard-line individual who vowed not to make the same perceived mistakes as his predecessor.