The setting is Valdolla, a large city completely surrounded by snow-capped mountains.Edward, Alphonse, and Winry meet Sophie Belkman, a fourteen year old girl with silver hair and light blue eyes who has been cornered by Leonid, the guardian of ice. When Edward's attempt to save her from him fails, she uses a strange power causing a blinding golden light to light up the entire sky.
Afterward, Leonid retreats, and Sophie passes out. The trio run to her aid. Soon after they've learned each others names, Sophie takes Edward and Alphonse and presses her seal, (A transmutation circle shaped like a flower) onto Edward's right hand, and Alphonse's shoulder, increasing their alchemic abilities.
They sought out the Guardians of Ice, Wind, Earth, and Fire to get closer to solving the mystery of Velza. During this time, they progress through an ancient castle, where on the balcony, Sophie experiences strange pulsations accompanied with voices that make her scream. A strange transmutation circle is inscribed in the ground right by a rock-like platform that has handcuffs hanging down from chains to suspend someone.
Ahead, the balcony overlooks the mountains. Sophie and the Elric brothers are surprised by Romeo Craigin, who are then taken into Custody by Venus Rosemaria and her subordinates Izzy Trigger and Boris Hammer. Edward yells for Sophie to escape. Alphonse is strapped to an Electrical machine for testing, and Edward stripped and locked in a cold jail cell with nothing but his boxers to stay warm, but Edward finds a way out and they escape the military base together.
Upon fighting and defeating three of the four guardians twice, the brothers discover that they lose their power, and wither away into dust. Sophie saves Leonid who has been lifted from his curse, but is only shot and killed by Romeo Craigin moments after the trio leave the area. The brothers' journey finally comes to a close after reaching the highest level in the Shrine of Velza, where they find Sophie who has been possessed by Velza because of the red rock that Zelgius placed in her chest, and break her out of the trance.
They fight Velza as a disgustingly ugly and enormous monster with a skull for a face. Upon defeating Velza, she gets sucked into the ground but re-emerges again in a human form covered with blood and glowing eyes, creating a massive vortex of wind and red light in her rage. Sophie approaches her, and despite the fact that Velza attacks her twice, she still survives almost unharmed (except for some bleeding on her forehead). Sophie then wraps her arms around the angry Velza, crying, and her words cause Velza to calm down, and she hugs her in return. Her eyes are shadowed out, but a tear falls and lands on Sophie's face where she begins to wither to dust. Her gentle eyes are revealed for a split second, and her last word being a "thank you" before vanishing for good.
Afterwards, all of the monsters that were summoned when Zelgius initially placed the red stone in Sophie's chest, vanished as well, leaving citizens and military soldiers alike thankful and relieved that the terror was finally over. Zelgius, who is standing on the balcony with Roy Mustang notices that everything's vanished, and after saying his final farewell, he sets himself on fire and disappears into the air. They return to the Church to find Winry and Sophie's beautiful white cat, Norn, and decide to have a nice walk in town since they no longer had anything to worry about.
On the way through the empty streets, Edward is pushed back by Winry, as she is deeply immersed in a conversation with Sophie, which causes him to fall behind the other three. In a shadowed alley, Toriga stands covered with a blanket, muttering and holding a large dagger. He has gone insane from his friends death by the flying monsters. The moment Edward reaches the alley, with his friends far ahead, Toriga lunges out and stabs Ed in the chest, then walks away, causing death on impact.
Alphonse, Sophie, and Winry turn around after hearing a thump from behind them and run to Ed's side, crying in shock. After seeing Ed lying motionless, Sophie decides to use her power to bring him back to life. She places her hands over the wound in his chest and a light starts glowing. She meets Edward (who is floating upside down) in a beautiful looking place with a sunset on one side and the daylight on the other and talks with him. Edward screams her name out before she vanishes, and realizes that he's alive again (reaching out for Sophie).
When he turns, he sees Sophie sitting with a blank and vacant expression, and Winry sobbing uncontrollably by her side. He then suddenly realizes that something is wrong, and moves to her, screaming and touching foreheads together. Edward and Alphonse meet Führer Bradley at the Headquarters which turns into a fight, where winning or losing will change the ending.
Upon losing the battle, Edward is struck unconscious by Major Alex Louis Armstrong where he and Mustang speak with the Führer, who then enters the HQ and kills Romeo Craigin. Winry and the Elric brothers try to speak to Sophie who is vacantly staring out the window not even aware of their existence. They leave Valdolla in grief and sorrow.
Mustang and Hawkeye are treated for injuries at the Hospital. At the very end, Norn continually meows trying to get Sophie to come back to reality, and just when hope seems lost, Sophie stresses out the words "Norn" and "Ed" with a smile.
If you win the battle the scene with Norn still plays out but she runs from the hospital to the train station, recovered. Although she first believes her friends have already left, she succeeds in reuniting with the gang.
