忍者の里・伊賀から忍術修行のため上京したハットリくんが、様々な騒動を巻き起こす物語。居候先の三葉ケン一との友情やギャグを描く一方で、様々な忍術を読者に紹介する要素も盛り込まれている。
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The story follows Hattori-kun, who travels to the capital from the ninja village of Iga to train in ninjutsu, causing all sorts of commotion. While depicting his friendship and comedic antics with his host, Mitsuba Kenichi, the series also incorporates elements introducing various ninjutsu techniques to readers.