毎日繰り返される日常生活のどこかに、不可思議な世界への入り口がある。これは「Y」の始まりの物語。ある日、寺刃ジンペイのクラスに転校生がやってきた。彼の名は小間サン太夫。二人は好きなアニメの話をきっかけにすぐに意気投合。すっかり打ち解けたジンペイは、コマに恋の悩みを相談する。なんでも、電車の中で会う女子高生に、なぜかドキドキしてしまうのだという。コマに協力してもらい、彼女に告白することを決意したジンペイ。次の日の放課後、声をかけるために彼女の後を追うが、何やら怪しい男が後をつけていることに気づき…
Somewhere in everyday life that repeats every day, there is an entrance to a mysterious world, this is the story of the beginning of the "Y". One day, a transfer student comes to the class of Jinpei Jiba. His name is Sandayuu Koma. The two of them immediately hit it off in the wake of their favorite anime story. Jinpei, who is completely open, consults with Koma-kun about his troubles of love. He says that he is for some reason in love with a high school girl who he meets on the train. Jinpei decides to ask Koma-kun to help and confess to her. After school the next day, they followed her to talk to her, but they noticed that some suspicious man was following her...
