The movie takes place after Ethan Hunt's successful mission in Mission: Impossible 2. Ethan is now retired and living a quiet life with his girlfriend, Julia (Michelle Monaghan). However, his peaceful life is disrupted when an old acquaintance, Owen Davian (Philip Seymour Hoffman), emerges as a major threat. Owen, a brilliant and deadly operative, has stolen a highly classified computer program known as "The Nightshade," which can locate and neutralize any target.

Mission: Impossible III (2006) marked the feature film directorial debut of J.J. Abrams, who brought a more personal and emotional tone to the franchise. The film follows a retired Ethan Hunt, now working as an instructor and engaged to a nurse named Julia, who is unaware of his true career.