Back at Central Command, Colonel Mustang scolds Edward for taking action without taking his target's abilities into account and explains once again that their quarry is Isaac McDougal the "Freezer", a former State Alchemist who had served during the Ishval Civil War, but quit the State Military and became a anti-government radical when the fighting ended. Meanwhile, McDougal has broken into Central Prison in order to recruit an old comrade, the incarcerated "Crimson Lotus Alchemist" Solf J. Kimblee, to his cause. Citing the mysterious atrocities that the State Alchemists were ordered to perform in Ishval, McDougal suggests that Kimblee's assassination of his superior officers during the war in protest to the military's shady activities, but Kimblee laughs him off and notes that he only murdered them because he wanted to and not for some idealistic principles. Disappointed, McDougal leaves by himself but returns to his work - drawing more of his unique Transmutation Circles around the city and remarking that his actions will be King Bradley's undoing.

The next day, the military efforts to find Isaac are redoubled and Mustang himself joins the search. As McDougal puts the finishing touches on his last circle, he is discovered and accosted by the "Strong Arm Alchemist", Alex Louis Armstrong. Their battle draws the attention of Ed and Al, who rush over to back up Major Armstrong, but Isaac escapes again. He is discovered by Colonel Mustang, who he identifies as the "Flame Alchemist" but escapes capture by using his ability to transmute water to counter Roy's flame alchemy. He heads to one of his many transmutation circles only to be met by the Elric brothers, who have deduced his location by noticing a pattern in his movements, but before they can engage him once more, the Freezing Alchemist puts his plan into effect and - with an odd new display of Alchemical power, causes each of his Transmutation Circles around the city to react simultaneously, erupting in gigantic, growing mountains of ice. Meanwhile, hidden from all sight, a mysterious being takes sudden and silent notice of the strange new energy's activation. As Ed and Al deduce that McDougal could only perform such remarkable new feats with the aid of the legendary Philosopher's Stone, the Freezer demands to know whether Fullmetal truly understands what Central Command is plotting for the country and flees again. McDougal's walls of ice continue to grow and shift despite the military's best efforts to stop them and Edward realizes that the Freezing Alchemist is attempting to create a gigantic glacial Transmutation Circle with military headquarters as its center. As Armstrong and Mustang work together to disable the circles on the ground, the Elrics go after McDougal and throw off his momentum. In the struggle, however, Isaac knocks off Al's helmet and realizes that the armor-clad boy is empty inside - a hollow suit of steel with a soul bound to it by way of a Blood Rune. Seeing this, he realizes that the reason for the boys' unusual bodies must be that they had performed alchemy's greatest taboo - Human Transmutation. Furious at Freezing's remarks, Edward attacks again and knocks McDougal to the ground, where he flees his pursuers by slipping once again into a back alley. Yet, before he is able to make a clean getaway, Isaac encounters King Bradley himself, who draws his sword and cuts the fugitive down with inhuman skill and speed. As McDougal's blood spills into the gutter, a small red stone floats along in the stream and turns to dust. The mysterious being from before notices the sudden cessation of strange energy and returns to the shadows.

In Reole, a mysterious woman and her stout companion learn of Isaac's death and remark that he would have made a good Human Sacrifice. The woman posits that the Freezer must have overused his stone and notes that her own mission will begin very soon.