When a high school girl gets a sudden transfer to the prestigious boarding school her parents went to, she expects her life has nowhere to go but up. She's immediately thrust into the school's complicated political dynamics, where she has to ask herself: who is that strange, menacing girl who keeps showing up? What is this student council that seems to rule the school from the shadows? Why does someone seem to have it in for her? And why does it feel like there's something about their past her parents aren't telling her?

Based on the classic anime Revolutionary Girl Utena, this game lets the player experience surreal school life at Ohtori Academy. Instead of having the player take control of one of the show's characters, the game's protagonist is a brand-new character meeting the cast for the first time. Players can make alliances (and enemies) as they interact with characters and settle in; the story branches based on how characters feel about the protagonist, with nine possible endings and an enormous number of branching story paths. A page in the player's student handbook shows the player how every one of the main cast feels about her, letting the player be strategic with the route they take through the game.

Utena captures the show's aesthetic with art and music taken directly from the show alongside new artwork, cutscenes and music which match the original show's presentation. All dialogue is fully voice-acted with the original actors from the show reprising their roles, alongside new actors playing the game's original characters.