The battle for the Capital city of Kyo rages as warring political factions vie for power against hereditary rulers. After the murder of her parents at the hands of her seditious uncle, a young girl named Kintoki flees to the mountains to lead a harsh life; she is renamed Kai Doh Maru by the local villagers. Rescued by Raiko, the Captain of 'The Four Knights' - honorable defenders who protect the peace of the city, she is raised within their group as a boy. Living among the Knights, she learns the practices of martial arts and develops into a skillful samurai, becoming a permanent member of their team. Now, as a young woman of seventeen, she begins to discover new feelings of passion and love for Raiko... but she also discovers that these new emotions cause a storm of jealousy and rage in another woman linked to her past.

Jesus Christ and Gautama Buddha, the founders of Christianity and Buddhism, are living together as roommates in a Tokyo apartment while taking a vacation on Earth. The comedy often involves jokes about Christianity, Buddhism, and all things related, as well as the main characters' attempts to hide their identities and understand modern society in Japan.

In a quicksand surrounded town called Makka, rumors spread of a legendary robber named Gasback is after the town. To protect it, Mayor Kepler has hired bounty hunters. These hunters have been following Gasback from town to town in hopes of getting the bounty. Vash the Stampede is in town, along with Meryl and Milly, along with the female bounty hunter Amelia and Nicholas D. Wolfwood.

One year after the events of the anime, Rintarou begins to feel the repercussions of extensive time travel, and eventually completely fades from reality. Kurisu, being the only companion to remember him, now must find a way to bring him back.

One year after the events of the anime, Rintarou begins to feel the repercussions of extensive time travel, and eventually completely fades from reality. Kurisu, being the only companion to remember him, now must find a way to bring him back.