Mahōtsukai no Yoru is a fantasy visual novel set in Type-Moon's "Nasuverse", a shared universe that also serves as the setting of most of the company's other products, including Tsukihime and the Fate series. The main story is completely linear, containing no branching routes, choices, or other opportunities for input from the player due to the fact that it is told from a third-person perspective. This story, which is set near the end of the Shōwa period in the late 1980s, begins when Aoko Aozaki, a high school student from the Aozaki family of mages, finds herself thrown into the world of magic after her grandfather spontaneously appoints her as the head of the family. She moves into an old mansion to be trained in the magical arts by a young witch named Alice Kuonji. When mysterious intruders appear to disrupt the magical field in their town, the two witches set out to discover the intruders' identities and motivations.
After the conclusion of the main story, the player can access a bonus chapter, "Potete dormire, ma nessun rida", which is told from the perspective of Kojika Kumari, a side character in the main story. In this chapter, the player (as Kojika) must periodically select a choice from several options on-screen to solve a murder mystery while trapped in Alice's mansion. This chapter concludes with one of multiple endings that can range from good to bad depending on the player's choices.