On their way home from high school, Tamahi and some classmates are shocked as they witness someone fall from the rooftop of nearby apartment. Panicked and confused, they rush to the building only to find it deserted. As Tamahi wonders about this, she has the uneasy feeling they are being watched. What is the strange presence around her...

Third-grader Himeno moves to a huge mansion in the country. However, she soon finds out it's a ninja house! The ninjas Akamaki, Aomaki, and Kiiromaki mistake Himeno for a princess and begin solving problems for her with their own unique skills. But that is not the full extent of their powers! When Aomaki and Kiiromaki combine, they form Midorimaki. Similarly, when Akamaki and Aomaki combine, they form Murasakimaki; and when Akamaki and Kiiromaki combine, they form Daidaimaki. Life with these colorful ninjas has only begun when they discover a large tornado heading for the mansion. What will happen to Himeno's family? Can the colorful ninjas protect Himeno?

Shortly after winning the World Martial Arts Tournament and using the winnings to pay off her grandfather's one hundred million yen debt, a reporter shows up on Kizuna Todoroki's doorstep. Impressed that such a young girl was able to defeat the 10-year reigning champion, the reporter wants to interview Kizuna for a piece on her and the Wadachi Ju-ken school of martial arts founded by Kizuna's grandfather. However, before the interview can end, challengers begin to appear at the Todoroki household. After hearing that Kizuna is only 12, they hope to defeat her before her 13th birthday to usurp her position as the world champion. As dozens of challengers appear, Kizuna struggles to bring them all down, while the reporter learns more about the Todoroki family.

Hundreds of years after the 20th century, nature and the ecosystem have been devastated due to use of nuclear and biological weapons. Most of the Earth has been contaminated and is collapsing into ruin, and a great majority of plants and animals are now extinct. The world heads to the "Big Six," the sixth mass extinction event. Humanity built cities in the sky, migrating the endangered species of animals and plants there. Over many years, the animals evolved in these isolated cities. With artificial genetic crossbreeding, they acquire language, bipedality, and build a life and civilization for themselves free from want. No one thinks of the world below any longer. One day, a single plant seed wanders into one of the sky cities, and the children Kui, Hiruma, and Root discover it. Unable to resist the temptation to look into the world outside, they decide to undertake an adventure to the outside world, unknowing that once they set foot on the ground, they will never be able to return.