The film is inspired by the events that took place at the Abu Ghraib prison in Baghdad, Iraq in 2003 during the Iraq War. The film follows a young soldier serving in the Army Reserves who gets transferred to the "Hard Site," a cellblock containing the most dangerous terrorists. At this site, the soldier witnesses the mistreatment of prisoners by military interrogators and members of the military police. 

Most of the film takes place in the prison, and the daily, boring, and routine life of the Army Reserve protagonist is shown. In fact, it was this boredom that prompts the man to volunteer to guard the "Hard Site." Boys of Abu Ghraib shows the mistreatment of the prisoners as punishment and as the result of the soldiers’ lack of trust in these men, set against the larger background of the CIA enhanced interrogation program.

The main character becomes friends with a suspected terrorist, a London-educated engineer, and  develops a friendship with him until he confesses his involvement in a deadly attack. Later the main character’s treatment towards the prisoner changes and he ends up abusing other detainees. Prison is shown as a place where friendships can flourish yet be quickly damaged, all while the American protagonist has the upper hand.