Someday a group of classmates will perform a charm at night after school—the Happy Sachiko charm. This paper doll ritual is meant to make them stay friends forever, but performing it incorrectly will lead them to be dragged down into a dilapidated phantom of Tenjin Elementary School, which had been torn down years ago. Trapped until they can reunite and perform the charm correctly, the students will have to solve the mystery of the haunted school in order to make it out alive. Before that ill-fated event, however, the friends led ordinary lives. Corpse Party: Missing Footage reveals an insight into the students' lives on the day before they were thrust into a waking nightmare. [Written by MAL Rewrite]

In the not so distant future much of the earth has been submerged under the sea or destroyed by earthquakes. At the center of the turmoil is the mysterious Orphan. Orphan may or may not be the original cause of the cataclysms. Orphan`s goal is to raise a ship hidden deep beneath the sea to the surface, but doing so would result in the destruction of all humans except for the small number which are loyal to Orphan. Orphan`s agents pilot mysterious mecha known as Grand Cheres, and search the world for mysterious, giant disks which occasionally appear, flying at high speeds and wrecking much of the countryside, or cities, when they hit the ground. After a dying disc almost kills Hime, a Brain Powerd is born from the disc. Brain Powerds are another type of Mecha, similar to but not the same as Grand Cheres. Hime becomes the Brain Powerd`s pilot, forming a symbiotic relationship with the living mecha and joins an International Organization dedicated to stopping Orphan, or at the very least saving humanity should Orphan succeed.

An innocent young man, Ikuroo, has a parasite known as Baoh implanted in his brain by an evil organization, Doress. The parasite makes him nearly immortal and gives him the ability to transform into a really powerful beastie when he's in trouble. Doress intends to use him in some sort of ploy for financial success, world domination, or something along those lines, but when they're transporting him on a train, a young psychic girl, Sumire (who's being held by the organization due to her abilities), sets him free and the two escape together. Of course, Dr. Kasuminome is the mad scientist behind the whole Baoh thing, and he isn't about to let his test subject get away and he has considerable resources (including some superpowered lackeys, as well as a small army) at his disposal.

A criminal group known as Demon Seed terrorizes Tokyo with its vast armies of mecha. The local police is afraid to confront them, but one person stands in their way: Maron Namikaze, a 13-year-old idol singer with a catchy voice and unbelievable superhuman strength.