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.

Set in the Meiji era, Kidou Shinsengumi Moeyo Ken tells the story of Kondou Yuuko, Hijikata Toshie and Okita Kaoru. These three are the daughters of former Shinsengumi members and, in the same fashion as their fathers were, they get called upon to protect Japan from its current problems. Much of their work deals with vanquishing the mysterious paranormal phenomena springing up ever more frequently in the Kyoto area and defending the city from any other dangers that may arise.

Sometime in the future, the world was completely dried up and became all desert. They had little rivers and lakes left, which villians and dangerous animals lived. Water has become the most valueable thing on the world. Whoever can control water will rule over the world.

10,000 years ago, acting as judge, jury and executioner, Dangaizer sealed the fate of mankind by reducing it to ashes. Slowly, mankind rebuilt their civilization and once again stands at its peak. Hiding amongst the survivors of mankind, the evil organization of Goma lies in wait for the return of Dangaizer. This time, it’s a race to stop the awakening of the 3 that can pilot Dangaizer and subjugate the world to their rule. Will the 3rd pilot learn her true destiny and awaken in time, or will the world find a new destiny in the hands of Goma?