Hattori-kun received a letter from Iga's father asking him to take his friends and return home for spring break. Hattori-kun leaves for Iga with his younger brothers Shinzo, Kenichi, Yumeko-chan, and others. However, a suspicious shadow stares at the group... He is a subordinate of the scientific ninja Mechamaro, who has replaced the power of ninjutsu with the power of science. Mechamaro was plotting to confront Hattori-kun in order to prove the strength of scientific ninjas. And in order to occupy Iga no Sato, Hattori-kun sends a fake letter...