Marisa Kirisame has always loved Youkai. Her friends were Youkai and at the start of the Youkai War, she gave them shelter in her cluttered home. After years without seeing them, her parents sign her up to stay at a boarding school in the outside world to protect her from the so-called dangers. Now, Marisa is determined to make friends with the Youkai at the Youkai school next door and learn the secrets of the elite academy.
Reimu Hakurei typically solves incidents, but when the Hakurei barrier suddenly breaks, revealing Youkai to the rest of the world, she doesn't have many options left and reluctantly takes refuge at a school that accepts humans and Youkai alike to be protected from the angry humans and learn how to make their magic stronger. But Reimu hears rumors of the Youkai on the other side being in danger. With this, she sets off to solve a deadly incident, The Youkai Genocide Incident.
Sakuya Izayoi was sent to this school on orders of her master Remilia Scarlet in order to protect her from the military after the Scarlet Devil and her staff. But the young maid is lost there, without being able to spend time with her mistress and unable to protect her from any possible threats. Paranoid, she tries to break into the other school which of course proves more difficult then it needs to be.
Youmu Konpaku can't remember a thing up until she came to the school. All she knows is that she loves Youkai and supposedly served one. With her memories gone, Youmu wants to find out about what happened to her and discovers a certain club of humans wanting to help the Youkai. With this, the girl joins them in order to unravel her past.
Sanae Kochiya was a god of the outside world before the Youkai War. Once she died, she would ascend to Youkai level and would continue to live. Of course, as a living God, the military was after her and she retreats to the school to keep her secret under lock and key from the rest of the world. But when she learns of other Gods in a similar position not getting the help they need, she joins Reimu, Marisa, Sakuya, and Youmu to free the Youkai from the school.
(Note that I don't own any characters and this is a high school AU. Some characters may not know each other and personality changes may happen.)