Munich, Germany, 1923. Two years have passed since Edward Elric was dragged from his own world to ours, leaving behind his country, his friends and his younger brother, Alphonse. Stripped of his alchemical powers, he has been all this time researching rocketry together with Alphonse Heiderich, a young man who resembles his own brother, hoping to one day find a way back home. His efforts so far had proven fruitless, but after lending a hand to a troubled gipsy girl, Edward is thrown in a series of events that can wreak havoc in both worlds. Meanwhile, at his own world, Alphonse Elric ventures deeper into the mysteries of alchemy in search for a way to reunite with his older brother.

A fugitive alchemist with mysterious abilities leads the Elric brothers to a distant valley of slums inhabited by the Milos, a proud people struggling against bureaucratic exploitation. Ed and Al quickly find themselves in the middle of a rising rebellion, as the exiled Milos lash out against their oppressors. At the heart of the conflict is Julia, a young alchemist befriended by Alphonse. She'll stop at nothing to restore the Milos to their former glory – even if that means harnessing the awful power of the mythical Philosopher's Stone.