The story of Prison Break: The Conspiracy is based on the first season of the TV series Prison Break.

The original story of the series is dedicated to the young engineer Michael Scofield and his elaborate plan to rescue his brother Lincoln Burrows, who was falsely accused of murder and is now awaiting execution in the Fox River prison.

In the game, however, the player does not control Michael, but a character who was not present in the TV series: Tom Paxton, an agent for "The Company", the main villainous organization of Prison Break. His mission is to get into Fox River prison and report to the company about Michael's attempts to escape with his brother. The original story serves therefore as a background for Paxton's experiences in the prison.

Prison Break: The Conspiracy is essentially a stealth game with hand-to-hand combat portions. Most of the game is composed of objectives given to Paxton by other inmates. These objectives, for the most part, involve sneaking past security guards, janitors, or hostile inmates, staying unnoticed at all times. If the protagonist is spotted, the player returns to the previous check-point and has to play the part of the sequence again. If the hostile character is an inmate, it is possible to fight him.

There are also other activities the protagonist can engage in when not being on a mission, such as lifting weights, getting tattoos, and fighting other inmates for money and other prizes.