Musashino, Tokyo. An elementary schooler repeatedly attacks people in the streets. Known only to the public as "Lil Slugger", none of the victims can recall the young boy's face and only three distinct details are left in their memories: golden inline skates, a baseball cap, and the weapon: a bent golden baseball bat. Detectives Ikari and Maniwa set out to track down the perpetrator and put an end to his crimes.

A terminally ill girl named Himari Takakura is miraculously saved from death by a strange spirit who resides in a penguin-shaped hat. However, in exchange for extending her life, the spirit tasks Himari's brothers, Kanba and Shōma, to seek out an elusive item known as the Penguin Drum with assistance from a trio of strange penguins.

In a world where memories can be stored like computer data, a young man named Kaiba searches for his lost memories and discovers a connection with a mysterious girl.

Five years ago, a string of grisly murders shook the city to its core and now the rumors have begun once more. Boogiepop... Everyone knows about Boogiepop: meet her one dark night and you are taken. People tell each other the stories and laugh: no one believes that she can possibly exist in this day and age. Still, strange things appear to be going on and the darkness is taking on many forms. Something is out there.