Without being noticed by almost anyone, there is a fierce battle between the Kanto region (Tokyo and surrounding areas) and the Kansai region (Osaka and surrounding areas) going on. Behind the scenes, there are ninja. Offspring of Kansai ninja are harassing people in Kanto in order to make Osaka the capital of Japan. Four girls are transferred to a high school in Tokyo. The girls really are the descendants of ninja, JK Ninja Girls ("JK" is short for "joshikôsei", which means "high school girl(s)"), who have been sent to Tokyo to protect the people there. Their mission is "to prevent Tokyo Tower from disappearing". However, it looks like the Ninja Grandpas (a ninja group with old farts) are haunting high school girls, and secretly planning to destroy Tokyo Tower. Four JK Ninja Girls now move in to find the girls who are possessed by the evil ninja from Kansai. One of the JK Ninja Girls, Noel Kirigakure, befriends Nozomi Ono from the same classroom... but Ono's true identity is Mosuke Sarutobi, a member of the Ninja Grandpas.