Inside the Khmer Rouge takes an in-depth look at the history, domination, and current status of the Khmer Rouge (a Communist regime) in Cambodia. The film features revealing interviews with soldiers of both the modern Khmer Rouge and those who fight in opposition. A comprehensive timeline of the regime's five-year occupation in Cambodia is dissected and includes a review of key individuals, ideologies, and locations where devastation hit hardest. Following this, the film takes a look at the effects on the Cambodian citizens upon the retraction of Vietnamese forces. Inside the Khmer Rouge continues to investigate the current tactics the modern Khmer Rouge implement and their attempts to persuade followers in order to rebuild and expand their regime. Oppositely, local forces or "jungle soldiers" discuss their devices for assuring the destruction and atrocities once caused by the Khmer Rouge never happen again.

Why are two modern Buddhist countries fighting over an ancient Hindu temple because of a bad French map from the early twentieth century? By documenting this modern conflict over an ancient temple this film addresses a critical question for our times: How does culture matter in matters of war?