This special takes place three years after the end of the original series. Makoto is homeless as a result of his mom selling out their shop and soon becomes involved in a ‘bone smasher’ case, in which someone puts homeless people to sleep and breaks their bones.

Ryo Morinaka is a university student and works part-time at a bar. He is bored with his daily life and exists in a state of torpor. One day, his friend Shinya Tajima brings the owner of a host bar over to the place where Ryo Morinaka works. Shizuka Mido is the owner of the host bar. Soon, Ryo Morinaka begins to work for Shizuka Mido at the members only host bar. He feels embarrassment initially, but he fulfills the desires of women and develops a sense of purpose.

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.

Naoto, the son of a wealthy family, suffers from Werner syndrome, a premature aging condition; Dai is an overweight child troubled by his penniless father's drunken violence; Jun, a gifted student, is the foursome's natural leader; and Tetsuro is average...