Fullmetal Alchemist has great side stories that either expand the lore or focus on developing the characters, but how they’re portrayed in each anime adaptations will give a different emotional response. FMA 2003 is generally darker in tone, has more graphic violence, and a somber tone compared to FMA: Brotherhood’s more toned-down violence, more slapstick humor, and more uplifting experience, like fewer cast members dying or suffering a permanent disability.

For example, Rose from Lior devoted her life to Cornello’s cult in exchange for Cornello to revive her dead lover. In the 2003 anime, Cornello invites Rose to a room where her boyfriend is supposedly in bed, covered by sheets, in the process of recovering. A silhouette appears and calls out to Rose and she regains her faith in Cornello and continues to stay loyal to him (this is also the reason why the citizens of Lior are loyal to Cornello). It is then revealed that the person behind the sheets is a defective bird chimera made out of hundreds of sacrificed birds that was made to do one thing: to control Rose by parroting her name. It turns out Cornello isn’t capable of reviving the dead because human transmutation is impossible and this opened Rose’s eyes to the fact that no one, not even alchemy, can bring her loved one back. In FMA: Brotherhood, they skipped this scene, resulting in a less emotional experience. But on the flipside, there are other moments that are portrayed better in FMA: Brotherhood than in the 2003 adaptation and has more stories to tell that the 2003 adaptation couldn’t provide.

FMA: Brotherhood compressed a lot of stories into about eight episodes so that it could finally continue with the manga storyline so the only way to experience these stories is by watching the 2003 adaptation. Ed’s State Alchemist exam, a more paced out Chimera story, the Yoki side story, and the Armstrong Household episode just to name a few, are reasons alone to check out FMA 2003.

Both FMA 2003 and FMA: Brotherhood start off the same tale of the Elric Brothers Ed and Alphonse from the quaint town of Resembool who committed a taboo: they tried to resurrect their deceased mother through human transmutation using alchemy. The transmutation of a human being failed and according to the laws of Equivalent Exchange, Ed’s left leg and Alphonse’s entire body were taken. In a desperate attempt, Ed brings back Alphonse’s soul and affixes it to a suit of armor in exchange for Ed’s right arm. Ed gets prosthetic limbs called automail and with Alphonse’s now-immortal body, the brothers devote their lives to alchemy and search for the legendary alchemic amplifier called the Philosopher's Stone. The brothers believe that attaining this mysterious stone will grant them the ability to restore Ed’s limbs and Alphonse’s body, but this will not be easy because the brothers will be delving deep into the dark side of alchemy and facing powerful inhuman foes called the Homunculi.

The first adaptation of Fullmetal Alchemist aired on October 2003 and was in the uncomfortable situation of only having a few volumes of the manga to work from. With the manga series still ongoing at the time, FMA 2003 needed to tell the rest of the story differently by introducing anime-only characters, an original ending, and a follow-up movie sequel, The Conqueror of Shamballa. FMA: Brotherhood, on the other hand, was in the comfortable situation of airing in April 2009 with a ton of manga material to use, and as a result, FMA: Brotherhood is faithful to the manga source.

To note a few differences, in the 2003 adaptation, the Homunculi are beings that were created through various failed human transmutations and consumed red stones that are similar to the Philosopher’s Stone to stay alive. This means the being the Elric Brothers created through the failed human transmutation of their mother is a homunculus. In FMA: Brotherhood and manga, the Homunculi are creations of a powerful being known as “Father” and they loyally do his bidding, like manipulating people to create Philosopher’s Stones or forcing people to commit genocide to cover his tracks. In the 2003 adaptation, the main plot revolves around the antagonist manipulating the Elric Brothers to create a new Philosopher’s Stone for their nefarious deeds, and in Brotherhood and the manga, Father uses the Elric Brothers and other alchemists who committed the taboo as a catalyst that, in part, involves eradicating human civilization to achieve omnipotence.