The Earth lies darkened and deserted. Despite the best efforts of the film's heroine, Hikaru, the evil-filled castle of Cephiro has taken over the world and stands in the center of a lifeless Tokyo. Before the ice-witch Alcyone can take her revenge on Hikaru, she is rescued by Lantis, a young man who seals her into a magical maze where she is challenged to prove her powers while her friends are hunted down by Cephiro's warlocks. Fleeing through the silent city, Umi and Fuu must seek out the sleeping Mashin; godlike creatures that will fuse with them to form giant warriors of awesome destructive power. But the Magic Knights are afraid, untrained and alone... will even the Mashin be enough to save them from the evil acts of Cephiro?

The technology to create powerful cyborg soldiers has been released for public use by the Berühren Corporation. Those outfitted with robotic parts are known as the Extended. Juuzou Inui, one such Extended, was created as a soldier and has no memories of his former life. But now, after the war, he runs a business that takes care of Extended-related incidents around the city. Rumors of a renegade Extended that kidnapped a child reach his ears; lo and behold, as Juuzo returns to his office, a giant robotic man with a boy on his back crashes in, asking for help. While Juuzou could just turn the guy in and be done with it, something about this situation is too fishy to ignore. It seems that everyone wants hold of this kid and, whether he likes it or not, Juuzou must find out why this Extended is on the run, how it connects to the Berühren Corporation, and just how far the treachery runs in this city. [Written by MAL Rewrite]

2500 years ago, in India, Siddhartha was born as a prince of the Shakya clan, but he gives up his position as a prince to see the world. While he travels he meets a strange boy named Assaji, who can predict the future and a monk with only one eye. Overwhelmed by the sufferings he witnesses around him, Siddhartha strives to restore peace. Meanwhile, Prince Ruri of Kosara begins his attack on the Shakya clan.

In the year of Tenpo 14, Yoi, monsters from another world attack Edo. Those who fight against them are members of Bansha Aratemesho. In public, Bansha Aratemsho is known as an organization to study foreign books. In fact, they are a organization dedicated to destroying the Yoi. These warriors are called Ayakashi. They gather information of odd events in the country, and are sent to destroy Yoi who appear. They are generally very strange people. For example, a guy who has lost his memory, a girl who dresses like a man. They have special powers with which to beat the Yoi. (Source: AniDB)