"Shion no Ō" centers on Shion Yasuoka, a young girl who becomes a professional shogi player after her parents are murdered in a home invasion. The traumatic event leaves Shion mute, and she communicates primarily through written notes. Despite her silence, Shion demonstrates exceptional talent in shogi, a traditional Japanese board game, and begins to climb the ranks of the competitive shogi world. Her journey intertwines with the mystery of her parents' murder, as she suspects the killer may be connected to the shogi community.

The narrative explores Shion's relationships with other shogi players, including Ayumi Saitō, a fellow female player who becomes both a rival and a friend, and Yasuaki Saitō, Ayumi's older brother and a former shogi prodigy who now works as a detective. Yasuaki takes a personal interest in Shion's case, believing the murder may be linked to a series of unsolved crimes. As Shion delves deeper into the shogi world, she uncovers clues that suggest her parents' killer may be using shogi games as a means to communicate or leave cryptic messages.

The series balances Shion's growth as a shogi player with the ongoing investigation into her parents' murder. It highlights the psychological and strategic aspects of shogi, often drawing parallels between the game's tactics and the unfolding mystery. The tension between Shion's pursuit of justice and her passion for shogi creates a compelling narrative, as she navigates the challenges of both the competitive shogi scene and the dangerous secrets surrounding her past. The story maintains a focus on Shion's resilience and determination, as well as the intricate connections between the shogi community and the unresolved crime.