Hikaru to Hikaru centers on Hikaru, the descendant of a long family line of ninjas. Though he has long trained in ninjutsu arts, he longs to master a technique that he has long had trouble with, the "Kunoichi no Jutsu," which allows a male ninja's body to transform into that of a female body. Without mastering this technique, Hikaru will never be acknowledged as a full-fledged ninja by his peers. In order to force him to get better, Hikaru's father orders him to enroll at a well-known all-girls school, and use what little skill he has in "Kunoichi no Jutsu" to hide his true gender and graduate from the school.