The character spends the next two episodes behind bars. As an inmate of Fox River, Bellick attempts to stay out of trouble but is bullied by the other inmates in the episode "John Doe", an inmate called Banks forces Bellick to bring him his dessert after meals, Bellick does this but Banks demands more from Bellick who subsequently attacks him and his entourage with a makeshift blackjack, he immediately is feared and respected by the other inmates because it appears that Banks is high up in the prison food chain. It is revealed in the episode ”The Message” that Banks and his crew have got their revenge on Bellick, because he has been brutally beaten overnight, he is also warned that there are many more beat downs to come. Bellick is deemed to be of some value to Agent Mahone, who secures his release from Fox River. Mahone, who is under blackmail by the sinister Company to ensure the deaths of the Fox River Eight, decides to use Bellick as his under-cover operative, without any paper-trail to connect him to Mahone. Bellick thus returns to his earlier subplot as a fugitive hunter. He immediately shows his worth by tracking down escapee Haywire in "Chicago." After being absent for one episode, Bellick then re-appears in "Wash" where he is assigned by Mahone to track down Sucre, which he does in the next episode. Learning that T-Bag still has the money, Bellick forces Sucre to help him track it down. Their plotline also intersects with Michael's in the penultimate episode "Fin Del Camino", as he also seeks to capture T-Bag. Bellick is later shot in the leg by T-Bag and then captured by Panama police. T-Bag again frames him for a murder, this time a Panamanian prostitute. In the season finale, Bellick is sent to the prison Penitenciaría Federal de Sona. In the last scene of the season, he is discovered by Michael at Sona prison, battered, and lying on the floor, under a bigger inmate.