Tokimeki Memorial brings together the twelve young girls from Kirameki High School, but revolves around the main girl, Fujisaki Shiori. The story starts at the beginning of the third school year, which is the last year before the main character can choose a girl and date her at the graduation.

Takeru meets the boy Jodis which is in trouble for theft. Takeru saves him shares the night with him, finding out that Jodis is a girl. Later she is been kidnapped and Takeru goes to rescue her.