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.

In the year Cosmic Era 0071, a wartime brawl between two mobile suits results in the destruction of a neutral country. Shinn Asuka finds his entire family killed as casualties of the violence, and swears his life toward a vengeful pursuit of the Earth's Natural forces, under the impression they were the ones responsible for his family's death. Shinn works his way up through the ZAFT military forces, eventually gaining access to the cockpit of the prototype Impulse mobile suit. Athrun Zala, a veteran of the recent war employed in the service of diplomat Cagalli Yula Athha, finds himself drawn into a new conflict between the Naturals and the Coordinators: human beings artificially enhanced before birth and hated by the Naturals for their biological advantages. As the new war rears its head and violence becomes inevitable, Athrun finds himself as a mentor to the bitter Shinn. Athrun must steer the young pilot towards a mindset of mercy before his rage and desire for vengeance consumes him.

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.

U.C. 0097, one year after the opening of Laplace's Box. Despite the revelation of the Universal Century Charter that acknowledges the existence and rights of Newtypes, the framework of the world has not been greatly altered. The conflict later dubbed the Laplace Incident is thought to have ended with the downfall of the Neo Zeon remnants known as the Sleeves. In its final battle, two full psycho-frame mobile suits displayed power beyond human understanding. The white unicorn and the black lion were sealed away to remove this danger from people's consciousness, and they should now be completely forgotten. However, the RX-0 Unicorn Gundam 03, which disappeared two years earlier, is now about to show itself in the Earth Sphere once more. A golden phoenix... named Phenex. (Source: Gundam.info)