Set in an alternate version of the Meiji Era, a boy named Sakamoto Ryunosuke returns to Kyoto from Shanghai with his monster (youkai) Nekomaru. The law states that in order to live freely with humans, a youkai must be liscensed. The Kidou Shinsengumi Co. Ltd. is responsible for the capture of unliscensed youkais but must fight with the Tsubamegumi, who resents the new law. It turns out that Ryunosuke is the son of the owner of the Shinsengumis.

In a time of darkness and barbarism, the Chantry has arisen - a religious order seeking to bring stability to a world corrupted by sinister magic. Led by the Divine, the Chantry's Templar warriors ruthlessly restrain the Mages and their magical cabals. But when the Templars fail, the most elite order of the Chantry takes charge - the Seekers!

Nadie is a bounty hunter with an attitude, and she's got a lock on her next target: Ellis, a young amnesiac girl who is a suspect in the murder of a famous scientist. Nadie manages to apprehend Ellis, but on a whim, decides to accompany her to Wiñay Marka, a place which supposedly holds the key to unlocking Ellis's memories and her mysterious past. However, Nadie cautions Ellis that this does not mean she will go free—once Ellis has found what she is looking for, Nadie will turn her over to the authorities. With Ellis's connection to a gemstone called the Inca Rose as their only guide, the two set off on their journey south through Mexico to search for the mysterious "Eternal City" of Wiñay Marka.

Renton, son of scientists, and Eureka, a girl who can't live under the sun, are raised together when very young and become very attached to each other. One day, Eureka is taken away. Powerless at the time, Renton vows to rescue her. He enters the military and is soon is assigned to the Independent Youths Unit 303 of the First Mobile Forces thanks to his exceptional performance alongside his Nirvash, a bio-mechanical armor/control system. Unknown to Renton, lies a plot to extinguish the alien invasion that is currently happening involving not only him, but Eureka too.