In the game, you play a student in a high school - I believe you're supposed to be the same guy from part 1, as you keep on having memories of the Marionette from the original game. One day, you stumble upon a pair of abandoned marionettes, one called Marine and the other called Maria. You take Marine under your care while a rival and all-together obnoxious classmate called Arese takes Maria under hers'. Arese is under the impression that marionettes are nothing more than robots with a heart made of computer circuits, but your experience with part 1, where you apparently managed to raise the original marionette to near human form, has you convinced otherwise, and you intend to prove Arese wrong.