The Philosopher's Stone is by sacrificing human lives... At the edge of a remote southern country, Ed and Al come in contact with a person who is in the middle of escorting a group of people. They learn from him the existance of an old man who knows the history of the Philosopher's Stone. Ed and Al now turn their attention to the town where that old man lives.
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In their search for information regarding the Philosopher's Stone, Ed and Al have delayed the departure of a train full of Ishbalites. They are told by Scar's master that there is an elderly man on the outskirts of Kishiur who may be able to help them. Using the water tower, Ed creates a diversion which allows him and Al to escape along with two Ishbalite boys who will take him to this man.
On their way to Kishiur, Ed and Al express their desire for Winry to go home and out of harm's way. Finally there, the dump looks like a war zone.
Searching for the man, Ed and Al are called out by Hawkeye who reveals the events leading up to the transfer of Ishbalites. Ed and Al are allowed to visit the old man who is under the protection of the military not their custody.
Outside, Winry is shocked to find the hatred the two children possess for those who betray the God of Ishbal. Trying to take their minds off Scar, Winry asks about their mother. As it turns out, their mother worked in a hospital run by Winry's parents...
Inside the tent, the old man tells Ed and Al that he learned the Great Art which lead to his exile as an Ishbalite. Then, they are shocked that the Great Art is really alchemy. He then tells them that there is little difference in the method to create the Philosopher's Stone. The only difference is the number of sacrifices needed.
The Philosopher's Stone is created by a skilled alchemist who manipulates the souls of the dead into the Stone.
This is what happened to Ishbal. The country was sacrificed by Scar's brother in hopes of reviving the woman he loved.
Scar, already an exile, decides to create the Philosopher's Stone in order to defeat those who keep Ishbal from eternal peace.
Speaking with Hawkeye, Ed and Al are given the circumstances to Yoki's death and come to the conclusion that it was the work of the Homunculus.
Ed and Al have decided to go after Scar in order to stop him from doing something horrible. Here, Ed and Al, Winry and Hawkeye, and the two Ishbalite boys part ways.
In Central City, Sloth gives the orders for Lust, Gluttony, and Wrath to once again go after the Elric brothers. At the house of Hughes, Winry is shocked to learn that he has passed away leaving behind Glacier and Elysia.