Haruto Kirishima led a peaceful existence in the countryside, away from the hectic pace of city life. Then Yuzuki Eba emerged out of nowhere in his life, having traveled from Tokyo to live with her family for a short time. Their time together left him fascinated with the memories of that little period before she unexpectedly vanished from his life, leaving him with many unanswered concerns. Kimi no Iru Machi begins when Haruto relocates to Tokyo to live with his sister in order to pursue a profession as a chef. In actuality, he longs to be with Yuzuki. However, things do not get off to a good start. When he arrives, he is misidentified as a burglar and attacked by his sister's next-door neighbor, Mishima Asuka.