Amy to Yobanaide follows the story of a high school girl named Emi who has fallen in love with her younger step-brother, Tomomi. On her eighteenth birthday, she decides to confess her feelings to him. However, their lives take an unexpected turn when debt collectors seize all of her father's possessions, and Tomomi mysteriously disappears. Determined to find him and share her feelings, Emi takes on a quest to locate her step-brother.

As she searches for Tomomi, Emi discovers an alternate personality within herself named Amy. While Emi is shy and modest, Amy is driven by a desire to fulfill her deepest fantasies.