In Doumori, an imbalance of spiritual forces threatens to plunge the small city into complete chaos. Thankfully, for the students of Doumori Elementary School, new teacher and exorcist Meisuke "Nube" Nueno is determined to prevent the malignant spirits—known as youkai—from accomplishing their evil deeds. The first student who catches Nube's attention is transfer student Hiroshi Tateno, who displays inexplicable outbursts of anger, often lashing out at his classmates. When they find out that Hiroshi is possessed by a youkai, Nube manages to free his student thanks to the demonic power sealed in his left hand. However, a youkai hiding behind the appearance of doctor Kyousuke Tamano bursts onto the scene and quickly abducts Hiroshi. Helped by his student Kyouko Inaba and his expertise in the occult, Nube quickly uncovers Kyousuke's sinister plans. Rushing to Hiroshi's rescue, Nube will show once more that he will stop at nothing to protect his beloved students against all supernatural threats.

Toto has been dreaming about adventuring with other people for as long as he can remember. Despite his hero title, he still remains without allies due to his timid personality. Therefore, when three women: Ciel, Anemone, and Goa suddenly request to join him, Toto is overjoyed. Unbeknownst to him, they are all assassins assigned to eliminate him! While Toto resolves to protect his would-be killers, the women fight over who can finish off the hero. As Toto remains oblivious of his new party members' true intentions and finds himself passing out every time he gets flustered, the four of them embark on their peculiar adventure into the greater world.

Due to frequent misadventures with the supernatural and her hectic school life, Nene Yashiro can barely catch a break until Kamome Academy's annual sleepover event comes around. Nene is excited to blow off some steam with her best friend Aoi Akane and the rest of her class at the get-together. Unbeknownst to her, the sleepover falls on the same date as Urabon, when the line between the dead and the living gets distorted, allowing wicked spirits to come out to the surface. When an evil ghost is about to attack her, Nene is rescued by a mysterious figure: Shinigami, the Sixth Wonder that can trap souls using his flute. In that moment, Shinigami takes notice of Aoi and abducts her to use her as a sacrifice that will close the barrier for good. Joined by Hanako-kun and Akane Aoi, Nene must embark on a journey into the deepest confines of the world of the dead to save her best friend before it is too late.

Legends tell of an invincible martial art known as Mutsu Enmei-Ryu, an unarmed style that allows the user to defeat any number of armed opponents using incredible speed and strength. This is the story of three generations of those who bear the name Mutsu, and their encounters and battles with the strongest fighters of their era.