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When a great demon fox attacked Hidden Leaf Village, a powerful man known as the 4th Hokage had sealed the demon inside a newborn named Naruto, who then grew up detested by his fellow Leaf villagers. As a child, Naruto is isolated from the Konoha community, who regards him as if he was the Nine-Tails. A decree made by the leader the Third Hokage forbids anyone mentioning the Nine-Tails to anyone else.

After accidentally killing a government official’s son in a fight, Mugen and Jin are seized, and are sentenced for execution. Fuu successfully saves the two warriors, and hires them to accompany her during her search for a samurai “who smells of sunflowers” which may lead to her father.

Yamato, Naruto Uzumaki, Sakura Haruno, and Sai are assigned on a mission to capture Mukade, a missing-nin. They all have chakra-knives, which are uniquely-designed trench knives that allow a ninja to infuse their chakra with it to produce an added effect. They set out for the once glorious historic ruins of Rouran, a city with one thousand towers and is located in the middle of the desert. They pursue and corner the missing-nin. Mukade's goal is revealed to travel to the past and take over the Five Great Shinobi Countries with the power of the Ry?myaku, an ancient chakra flow deep underground Rouran. He unleashes the power of the Ry?myaku, which is seen to have been sealed by Minato Namikaze, Naruto's long-deceased father (who was well known as Konoha's Fourth Hokage)'s hirashin kunai, causing a light to envelop Naruto and Yamato, who was trying to stop Mukade. Sai stops Sakura from getting sucked in by the Ry?myaku by grabbing her onto his ink bird and flies to safety, leaving Naruto and Yamato in the mysterious light. Naruto and Yamato are sent twenty years into the past. When Naruto awakens from this time slip, he meets the queen of Rouran, S?ra.

Kagome Higurashi, a normal 15-year-old girl, falls down a dry well--and finds herself in the feudal past, 50 years after her ancestress Kikyo imprisoned the half-human/half-demon Inu-Yasha. As the reincarnation of Kikyo, Kagome possesses a magic jewel that greatly increases the power of demons. Kagome fetters Inu-Yasha with the help of her priestess-ancestor Kaede, and when the jewel is shattered Kagome and Inu-Yasha must ally to recapture the fragments.

The story follows Rico, an orphan who dreams of becoming a great cave raider, much like her mother, and solve the mystery of the Abyss. The Abyss is an unexplored enormous cave system inhabited by strange and wonderful creatures, along with mysterious artifacts. Generations of bold adventurers have been drawn by the cryptic depths of the Abyss, and over time came to be known as "Cave Raiders." One day exploring the murky depths she stumbles upon a little boy, who turns out to be a robot.