One of the most striking differences lies in the story arcs. The 2003 anime starts off faithful to the manga but eventually diverges into an original storyline. It introduces new characters and plot elements, such as Dante, who becomes the main antagonist. The Homunculi in this version are portrayed as the resurrected results of failed human transmutations, giving them tragic, human backstories. This adds emotional depth but diverges from the manga, where Homunculi are artificially created by Father, a being with godlike ambitions and a direct connection to the origins of alchemy.

Tonally, the 2003 anime is darker, slower paced, and more introspective. It emphasizes themes of loss, identity, and the consequences of obsession. Meanwhile, Brotherhood maintains a balance between action, humor, and drama, with a faster pace that mirrors the manga’s rhythm. The manga and Brotherhood also offer a more satisfying and complete resolution, whereas the 2003 anime ends on a more ambiguous and somber note, leading into a sequel film, Conqueror of Shamballa.

While both adaptations tell the story of Edward and Alphonse Elric, they do so in distinct ways. The original anime explores a darker, alternate path, while the manga and Brotherhood present a more expansive and faithful version of the creators’ vision.