Set in Tokyo's otaku mecca Akihabara, "Akihabara@DEEP" tells the story of five otaku who drop out of society and end up founding their own successful IT venture called Crook. But Nakagomi, president of an influential electronics company called Digital Capital, will do anything to get his hands on Crook.

In 1980, Ayuko is a new transfer student in Okayama from Tokyo. She doesn't have any friends and relies on her boyfriend Hideo who is a college student. Ayuko likes to draw a romance manga of herself and her boyfriend. Ayuko's classmate, Takemi, becomes a huge fan of Ayuko's manga and they become close friends. Due to an incident though, they drift apart. 30 years later, Ayuko is now a manga artist and comes back to Okayama to give a lecture at her former high school. There, Ayuko meets Takemi who is now a teacher.