Himeno, a third-grade student, relocates with her family to an expansive, aged mansion in the countryside. Initially distressed by abandoning her friends and city life, she soon uncovers three miniature ninjas residing there: Akamaki, specializing in fire; Aomaki, commanding water; and Kiiromaki, skilled in carpentry. Mistaking Himeno for royalty, they vow to resolve her difficulties using their elemental and craft-based abilities.

These ninjas can fuse into enhanced forms: Aomaki and Kiiromaki merge as Midorimaki; Akamaki and Aomaki combine into Murasakimaki; and Akamaki and Kiiromaki unite as Tōmaki (alternatively called Daidaimaki). When a massive tornado endangers the mansion, Himeno and the ninjas confront the threat to shield her family from destruction.