Rei Kiriyama is an extraordinary shogi player. Among the few elites to have gone professional as a middle school student, he is considered a genius. But what lies behind his prodigious facade is a teenage boy who suffers immense pressure from both his family, and from the high expectations from the shogi community. Rei moves out to live a more independent life away from his family, but his unorganized lifestyle and unsociable personality show no signs of improvement.

However, in a twist of fate that will prove to be a turning point in his life, Rei then encounters the Kawamoto sisters—the motherly Akari, the passionate Hinata, and the energetic Momo—who take great care of him. 3-gatsu no Lion tells the story of Rei as he reshapes his melancholic life and picks up the courage to begin facing the problems he evaded during his past.