One day, Kenichi meets Yuri, a foreign girl who is being chased by someone. In front of Hattori-kun and the Perman team, a mysterious masked monster named Psychoman, who can also levitate, appears. Psychoman, who plans to use his supernatural powers to conquer the world, forms an esper army of his own kind...

The monster Zippo, who had an ominous prophetic dream and came to Tokyo worried about his childhood friend Hattori-kun, witnessed countless pink eggs raining down from the sky. It is the egg of a monster sent by invaders who are trying to consume the earth's plants for energy. Hattori-kun and his friends struggle to repel them with the help of Perman who rushes in?

Kanzo Hattori, an apprentice Ninja, leaves his home town of Iga for his final training. He must go to the city of Edo (Tokyo), and the first person he meets shall be his master, whom he must protect with his life, whilst upholding the ninja code. Also while in Edo, Hattori must find out why their rivals, the Koga Ninjas, are flourishing while the Iga Ninjas are dying out. Hattori's master is Kenichi, a 9 year old boy. Kenichi is an introvert and not very popular boy, so he never plays with the other children from school. Kenichi also has a secret crush on a young lady called Midori, yet he's too shy to speak to her. Though as he watches Hattori trying his best, he too begins to try. Meanwhile, people are being found unconscious, their bodies completely unmarked. All the victims have a tattoo (the Koga Ninja crest) and are found with a throwing knife lying close by.

Kanzo Hattori, an Iga ninja, and his younger brother Shinzo are training in Tokyo. Kenichi, an elementary school student, lets the two of them stay and lives with them as if they were brothers, and one day he steals a picture diary written by Hattori (Kanzo). What was written there was that Shinzo became friends with a cute girl, Shinobino Ohime, and began to develop a relationship with Robomaru, a robot ninja of machine style ninja...

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...