Edward and Alphonse arrive in the city of Lior to deal with Father Cornello and ask him about the Philosopher's Stone. However, just as soon as the two brothers defeat him, Father Cornello is pulled into a dark void and disappears. Edward notices a strange phantom-like woman hiding behind the statues watching the scene. Shortly afterwards, after facing off against Bald, investigating Shou Tucker's home, and barely escaping death at Scar's hands, Edward and Alphonse return to Resembool for repairs. Healed, they investigate rumors of monsters appearing at a cave, coming across "monsters"; they come across the Phantom again, badly burning her. An alchemist appears and heals her, without using a trasmutation circle; they both vanish.
Reporting this incident to Roy Mustang, he reveals that similar creatures have been appearing all over Amestris; in addition, people have been disappearing. He sends the brothers and Lt. Riza Hawkeye to investigate a recent sighting; they find the village empty, and a bloodstained transmutation circle. Following a howl to a graveyard, they meet archaeologist Arlen Glostner, who is being attacked; after they defeat the monster, the same mysterious alchemist appears again. Arlen identifies the man as Jack Crowley; Crowley then vanishes again, seeming sad by the encounter. Arlen reveals he studies the ancient civilization of Lebis, and Crowley was once his friend. Crowley teamed up with Arlen to study the art of creating Golems (the monsters they're battling), hoping it would help revive his lost love, Elma, after failing with alchemy; they succeeded in bringing her back in a Golem body, but she reverted to dirt after a few months. Crowley went mad, bringing Elma back repeatedly against her wishes; Arlen left Crowley, unable to stand what became of his friend.
Arlen leads them to city of Siam-Sid, where Crowley is hiding out. They meet Elma, who tells Arlen it's not his fault for her pain, and that Crowley only keeps bringing her back out of love. When attacked by Golems (who disguised themselves as natives), Ed, Al, Riza, and Arlen are saved by the timely arrival of the military. Infiltrating the Tower of Lebis to find Crowley, the brothers get separated from Mustang, Hawkeye, and Armstrong. Choosing which one to go after, the brothers fight more Golems and come to the conclusion they may have to kill Crowley to put an end to the Golems' terror. Arlen arrives and gets transported away with the brothers to the Queen's Chamber; there, they defeat the Phantom, revealed to be the Golem form of Elma, who Arlen stay behind to mourn.
Ed and Al reach Crowley in the King's Chamber, where they attempt reasoning with him to no avail. Defeat, Crowley draws on the power of the Crimson Stone to become stronger; this reveals he became a Golem himself, to escape his sickly body. Even reduced to sludge, Crowley reanimates as an amorphous creature; Mustang, Hawkeye and Armstrong arrive, taking Crowley's attention away from the Elrics. They rush down the corridor, finding the Crimson Stone; touching it, Ed sees the memories of the King of Lebis and Crowley, who both caused destruction and death out of love. Using a transmutation circle Crowley left before going mad, they destroy the stone; Crowley and Elma are released from their Golem bodies, while Siam-sid is reduced back to ruins, and all the remaining Golems melt into mud. Arlen elects to remain in the city, having decided to live out his remaining years in the place he spent with his friends. Spectating the events from afar, Humonculi Lust, Envy and Gluttony say they received enough crimson stones from Crowley before he got caught up in bringing back Elma for good.