Ed struggles to overcome his mistrust of his estranged father in order to receive help in fighting Pride, while Mustang leads an attack in Central City.
The Elric brothers pass up the chance to enter the open portal and get their bodies back after learning the homunculi's ultimate plan to turn all of Amestris into an alchemical bloodbath on the "Day of Reckoning." To build opposition to the homunculi-corrupted military, Al asks his father for information about the homunculi's origins while Ed joins forces with a familiar homunculi whose conscience is bothering him.
Automail engineer Winry is captured and held hostage to force Edward to do her captor's bidding, and Hawkeye discovers the disturbing truth about President Bradley's son.
Ed, Al, and Winry return to Central Command and are greeted with the bad news that Lieutenant Colonel Maes Hughes has been murdered, and Colonel Mustang is out for revenge.
The raid on the Devil's Nest becomes a slaugter as government troops exterminate the Homunculus Greed, and foreign travelers arrive in Amestris looking for the Philosopher's Stone.
Ed, Alphonse and their mechanic Winry go south in search of Izumi Curtis, the master alchemist who taught the brothers how to use alchemy, but an encounter with a pickpocket turns them down a different path.