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Hailing from the mountains of Iga, Kanzo Hattori moves in with elementary school student Kenichi Mitsuba and his family to hone his skills as a ninja.
Kenichi is just an ordinary boy until he met Hattori who is a ninja. Because of his helpful nature, Hattori along with his brother Shinzo and his ninja-dog Shishimaru stayed in Kenichi's house and inevitably changes Kenichi's daily life with the infusion of the ninja background he comes from.
Way out in the sticks, the fourth-graders of the local school in Tokio village all have their own superpowers of doubtful merit, including flying eyeballs and missile-hair. Ippei and his friends study hard to be ninjas, but they are constantly under treat from the arrogant cheats from the neighbouring village of Techno.
On a school trip to the Ancient Capital of Nara, Ataru and the rest of his classmates are walking around on a town tour when suddenly a ninja girl named Kaede dashes by and drops a very important scroll. Ataru, being the klutz and womanizer that he is, goes to chase her but trips on the scroll and picks it up. Now, with Lum standing in her way, Kaede must race to get the scroll back from the clueless Ataru – but will she succeed, given that she now has reasons to doubt her own ninja skills?