Millie is thrown to Barry, the son of her mother's best friend in the name of helping her with her poor grades. She is totally at a loss while Barry is pondering over how to drive her away. In this way, the two who do not know each other and are different in character are forced together for a long time to come. Kabedon? Sleep in the same bed? Isn't it a simple co-living for tutoring?

Rokujou Miharu is a boy who has a hijutsu (hidden technique) living inside of him. This hijutsu is the power of creation. Many ninja clans are seeking it as the one who possesses it becomes the ruler of the ninja world. Rokujou’s classmate Kouichi started a nindou (“Way of the Ninja”) club at school with Kumohira, his English teacher. Both Kouichi and Kumohira are secretly ninjas. They tried to persuade Rokujou to join the ninjutsu club. At first, he was reluctant, but after being attacked by group of ninjas trying to get his hijutsu, he joins. He must become the Ruler of Nabari in order to survive.

Silent, apathetic yet mischievous, 14-year-old Rokujou Miharu is the bearer of the hijutsu, "Shinrabanshou", a powerful technique many ninja clans desire to possess to become the ruler of Nabari. Fellow classmate Kouichi and his English teacher Kumohira are both secretly Banten clan ninjas, pledging themselves to protect Miharu from his many attackers. Keeping apathetic, Miharu attempts to reject their invitation to join their ninja ‘club’ however, after numerous attacks; he finds no choice but to join their group as a means for his survival. Slowly, Miharu takes a step closer to becoming the ruler of Nabari.

Two years have passed since the Great War. Akito and Yurika have vanished. The Jovians and the Earthlings have joined forces and Ruri is now captain of Nadesico B. As the popularity of Boson Jumping grows, a vast transportation network has been developed. Dubbed the Hisago Plan, this network of Chulip portals holds the answers to the mysteries behind Bose particles and their power. If those secrets should fall into the wrong hands, it could mean big trouble. And big trouble there is. A Martian splinter group has launched an offensive, leaving the United Forces befuddled and desperate. So much so, in fact, that the former crew of the Nadesico is called back to active duty for a special unsanctioned mission-to save us all. Does this menagerie of misfits have what it takes? Who will win the race for the Boson technology? And what the heck happened to Akito and Yurika?