Shion no Ou follows the story of Yasuoka Shion, a 13-year-old Shougi player with a past of tragedy. Shion's parents were brutally murdered in front of her when she was 5 years old. The murderer sat down with her and challenged her to a game of Shougi, after telling her that if she wanted to stay alive she should forget how to speak, and forget what happened that night.

Now Shion has entered the realm of female pro Kishi, mute but strong. As her playing gathers more and more attention, so do the questions about her past and the brutal murder she witnessed. Shion's memories slowly come back, and the mystery begins to unravel, thread by thread.