Hearing a rumor about the Philosopher's Stone, Edward and Al head to the City of Gold, Xenotime. Before its decline, the town was known for its prosperity and wealth. As a last resort to restore their prosperity, the research of the Philosopher's Stone was entrusted to a pair of siblings acting as the Elric brothers...
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Upon their arrival in Xenotime, Ed and Al hear cries for help. They discover a young girl named Elisa who is has been trapped by a falled mine cart. Using alchemy, Ed transmutates the cart into a block a iron.
That night, the two brothers are treated to a grand feast at the local tavern. A man by the name of Vercio bursts into the tavern inquiring about Elisa's well-being. However, he is met with hostile words from her father because Mr. Vercio made Elisa work in the mines of Xenotime.
After his departure, a villager mentions that the Philosopher's Stone will soon be completed, and Elisa's dad asks whether or not Ed and Al have come to help with his research. Realizing that things have become a little more complicated, Ed decides to meet with Magwar.
When asked their names, they are met with surprised looks. It seems that imposters have assumed their identities.
In order to find out who it was that stole their identities, Ed and Al head to the mansion built into the hillside. The mansion is heavily guarded, and the brothers are forced to sneak inside. Once inside, they promptly begin their investigation of the mansion. However, they are interruped by the imposter who seems to posses incredible powers of transmutation. A fight ensues, but when the guards arrive, Ed and Al are forced to escape.
Deep within the mine, Magwar stands at a fountain of red water. He is ordered by Envy to finish the Stone soon. Back outside, Ed and Al are taken in by Mr. Vercio. In the morning, Ed goes out for a walk, and Al goes to the pharmacy for Elisa's medicine. Unable to buy the medicine, Fletcher, the younger imposter buys it for him. Spending time together outside, Al learns that the father of the imposters spent his entire life researching the Stone.
Infiltrating the mansion once again, the brothers end up in a hallway with a gutter filled with red water said to be the source of the Philosopher's Stone. Ed passes out due to fumes rising from the red water. Fletcher reveals some startling information: the reason many people are coughing is because the red water is dangerous to humans.
Fletcher's older brother appears, and a rematch between him and Ed errupts. Ed slips in the pool of red water forming from the imposter's attack. However, he is saved by Fletcher who realizes he is the only one who can stop his brother.