Edward Elric (voiced by Romi Park) finds himself stranded beyond the Gate in Munich, Germany, in the year 1923. He works as a rocket engineer alongside Alfons Heiderich (Shun Oguri), the real-world counterpart of his younger brother. Meanwhile, in Amestris, Alphonse (Rie Kugimiya) searches for a way to bring Edward home. Edward also rescues Noah (Miyû Sawai), a Romani woman being pursued because of her ability to read minds. He foils the plans of a rogue alchemist named Huskisson (Unsho Ishizuka) before the story moves forward in time. The pro-Nazi Thule Society, believing that Amestris is the mythical paradise of Shamballa, then attempts to tear open the gateway between the two parallel worlds.

Originally released in Japanese cinemas on 23 July 2005, the story later received a continuation in the original video animation (OVA) Kids. The film serves as the official conclusion to the 2003 Fullmetal Alchemist anime series, which follows an original storyline that differs from Hiromu Arakawa's manga. The Indonesian Film Censorship Institution (LSF) has classified Fullmetal Alchemist the Movie: Conqueror of Shamballa for audiences aged 13 and above. (air)