In this school comedy, a girls' high school suddenly goes co-ed, but the incoming boys are far below their expectations. As a result, some of the girls start a project to reform the boys into "princes."

Akihabara is a Tokyo district full of manga, anime, electronics, video games, figurines, etc. It is a place that gathers fanatics of such themes, people who are commonly referred to as otaku. Page, Box, Akira, Taiko, Daruma, and Izumu are six otaku each with his/her own troubles and sought relief through a website called "Yui's Lifeguard." When site owner Yui died of a mysterious death, the six who are each experts in their own fields gathered to form "Akihabara@DEEP", a "trouble shooter" group that vows to protect Akihabara and solve the problems of its inhabitants.

Yumi, a writer of a science magazine, witnesses a mysterious death of a high school girl who received a "one missed call" from her own cell phone, two weeks in the future. The disturbing message on the cell phone turns out to be the screams of the victim.