"One Last Crane" is a visual novel centered on Yuuki Murakami, a boy who has a brain tumor. After a long year of treatment without any positive results, Yuuki asks for his final wish: to return to his hometown and fulfill his promise to meet again with his childhood friend, Saki Nishimura. However, as always, things are hard for him.

Saki no longer lives where she used to, and no one knows her whereabouts. The last hint Yuuki got was from the high school Saki had said she wanted to attend—Shimizu High School. Together with his adopted little sister, Mary, and his new tomboyish neighbor, Chihiro, Yuuki keeps searching for the girl, only to meet Asuka Fujimoto, the most popular girl at school, who happens to look like Saki.

Not once has Yuuki doubted that Asuka really is Saki, but Asuka gives him the cold shoulder without admitting that she’s Saki. Could she really be a different person? Faced with the prospect that his life could end soon, Yuuki is determined to find Saki, even within another person.