Excitement runs high at Mahora Academy as the girls of Class 2-A prepare for their annual school trip. But poor Negi Springfield has more than Kyoto fun on his plate, for one of his students appears to be missing! Sniffing a newsworthy story, the class reporter proves how truly transparent some girls can be...

To make matters worse, their planned outing quickly develops into a bizarre hostage situation, and a mind-boggling homecoming sets Negi's world spinning. It seems some of the girls have been keeping secrets even bigger than his own!

As the new-found academic allies mount another rescue mission, Negi fears tat they might not quite add up. But all math aside, ancient Kyoto serves as a bittersweet backdrop for friendships, both old and new, as one suffers in silence and another proves unable to breach the rivalry.