The characters from previous .hack//G.U. Games and .hack//Roots receive an email from Ovan. He is requesting them to go to Hidden Forbidden Festival where is set up a mysterious summer festival. There they find an AIDA Chim Chim who wishes to peacefully co-exist with the other players of The World. It then transforms into the word "Returner", so they assume it to mean that Ovan will return to The World.

The story focuses and revolves around the 108th Guard Squad, stationed in Aomori. A poorly equipped unit with very little military standing, it is often viewed as a 'reject camp' for pilots not making the grade for the elite units based in Hokkaido. The apparent helpless nature of this force is hardly a deterrent for the encroaching enemy armies, ever closing in on both the 108th and the rest of the empire. The young pilots of the 108th, who had dreamed on returning home, are plunged forcefully and unwillingly into a war.

Cosplay City is in danger when the evil Dolmeck shows up. Commanding his army of monsters, he plans on destroying everything. Only one person can stop this: Cutey Honey. After she is released from her dormancy, Honey Kisaragi becomes the multi-transformational android Cutey Honey. However, the least is expected when Honey is faced with an old enemy from the past: Panther Zora.

Hideo Ozu is an editor in a shady adult video company. For years, he has dreamed of being a motion picture director while his childhood friend Mai Kurosawa has become an upcoming actress. Then one day, his dreams are shattered when Mai takes all of his amateur videos of her and tells him to get out of her life. On his way home after a few drinks, Hideo bumps into Cyberdoll Sara, who makes him mark an invoice. When he arrives at his pad, Hideo is greeted by three Cyberdolls - Mai, Ai and Mie. All three of them happen to look like different age variations of Mai Kurosawa. And when Kurosawa announces the release of a biography video of her using Hideo's old footage, Hideo decides to start his directing dreams over again using his three Cyberdolls.