After the decline of the once robust fields of science and technology, a new energy source known as magic fuels the modern era. Humanity creates forbidden biological weapons: Gears. Those Gears eventually stand against humanity in a rebellion. Although they manage to overcome in the struggle for survival known as the Crusades, humanity’s losses are so great that even after several decades pass, their emotional wounds remain unable to fully heal. Sin Kiske, the child of a human and a Gear, heads to his father Ky and mother Dizzy’s wedding ceremony. Their wedding breaks the ultimate taboo: a union between a human and a Gear. Even with the world at peace, it took many years for such a ceremony to come to fruition. Despite the complex array of emotions surrounding it, the wedding ceremony is met with blessings. When suddenly, a mysterious girl appears… The fated child inheriting Gear blood–and the mysterious girl who despises Gears. Their meeting would shake the world.

In the kingdom of Xoana, Lina Inverse and Gourry Gabriev unexpectedly come across their old companions, Zelgadis Graywords and Princess Ameilia Wil Tesla Saillune. Upon their reunion, the friends end up easily foiling the King of Xoana and his daughter's dastardly plans of world conquest.

Soon after, it is revealed that Zelgadis is in search of the world's most valuable magical tome, the Claire Bible, hoping to discover a method to recover his human body among the many secrets sheltered within it. Despite his protests, the rest of the group decides to join in the quest after hearing of his mission. However, just when they were wondering where to start looking for the legendary book, they stumble upon a mysterious priest by the name of Xellos, who claims that he may be of some help in their pursuit.

Set in Akihabara, the shopping area has been invaded by creatures known as "Synthisters" who prey on the patrons of Akihabara, feasting on their social energy and will to live. These enemies can only be stopped by direct exposure to sunlight, meaning to defeat these synthisters their clothes need to be ripped off exposing them to sunlight.

An Urban Legend describes monsters known as "bagurimono" lurk in dark corners of Akihabara, the paradise of anime. When Tomotsu Denkigai encounters one, he is almost killed but saved at the last moment by a girl name Matome Mayonaka, who repells the attack and later revives him.