The player does not control Michael, but a character named 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 as a background for Paxton's experiences in the prison.
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.