The story of Fullmetal Alchemist: Final Transmutation (also titled The Final Alchemy ) serves as the epic conclusion to the live-action film trilogy, adapting the final chapters of Hiromu Arakawa's manga.

In a climactic act of brotherly love, Alphonse sacrifices his own soul to restore Edward’s original right arm. With his limb returned, Edward delivers the final blow that forces Father back to the Gate of Truth, where "Truth" himself drags the villain into eternal void for his arrogance.

As the eclipse begins, Father successfully activates the circle, briefly attaining godhood. However, the tide turns due to a counter-alchemical circle planted years prior by Van Hohenheim and a separate effort by Scar to activate a circle that returns the stolen souls to their rightful owners.