The Protagonist spends several years in a coma in the prison infirmary, where he undergoes facial surgery to prevent disfigurement from the boat explosion at the end of Saints Row. Soon after waking from that coma, he escapes with fellow inmate Carlos Mendoza.
The Protagonist returns to the island when he triggers a prison break in order to rescue Laura, the drug dealing housewife from Saints Row. Guards use Tombstones and NR4s to suppress the riots, whilst many prisoners are beaten with Nightsticks and sprayed with Pepper Spray and shot with Stun Guns. Laura and The Protagonist successfully escape, although in the midst of the chaos.
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When not in a mission, all areas are accessible. The roof entrance is covered during "File in the Cake".
Both men and women appear to go to this prison, which isn't a natural occurrence in real life as men and women have their own prisons and aren't put together. The only known female inmates include Laura, The Protagonist and Shaundi, who says that she met Laura while in jail. There are also generic female prisoners appearing in "File in the Cake" and in the audience of the Prison Fight Club.
There is a ward for the criminally insane next to the main gate, this in real life would not happen as facilities for the criminally insane are in different locations from a normal prison.
It is likely that the prison existed during the events of Saints Row. There are many things that suggest this:
The penitentiary has an old, run-down appearance with rusty metal, moldy walls, an old generator, cracked cement and many more signs of age and/or wearing. It is unlikely that Stilwater Penitentiary was built after Saints Row or before Saints Row 2, since it would be only a few years old, not long enough for the entire prison to be in such bad shape.
In the prison yard there is an Vice Kings gang tag. While the tag may have been put there after the fall of the Vice Kings, the tag appears to be very old. There is also a Westside Rollerz tag in the prison yard.
There is a randomly spawning harmonica playing inmate Action Node in the yard.
This interior is located beneath the prison itself, and while the floor is solid, the walls are not. There are a few visual differences, most notably the west corner of the room is missing the television and a piece of rail from the wall.