Big Order begins ten years before the main story, when a fairy named Daisy appears before the child Eiji Hoshimiya and asks him to state his one and only wish. Whatever Eiji wished for remains a mystery, but the consequences are catastrophic. In the event later known as the Great Destruction, the world starts to fall apart as everything collapses around it, and countless people die.
Years later, Eiji is a high school student whose only concern is his sick sister. He no longer remembers what he wished for, only that his wish caused the Great Destruction. In the years since that disaster, thousands of other people have also awakened abilities that can make the desire in their hearts come true. These people, known as Orders, are widely feared and hated by the general public as dangerous beings.
Yet the danger around Eiji is more personal than public suspicion. Some of these Orders are hunting him in revenge for those he killed, turning his life into a string of relentless assassination attempts. As he fights to survive, Eiji is forced to confront the biggest mystery of all: what did he wish for, and what was he trying to achieve when that wish brought so much ruin to the world?