Japón en 2011, donde se ha eliminado toda la cultura otaku. Otaku Hero, el joven líder del Ejército Revolucionario Otaku, que se atrincheró en Akihabara y resistió la opresión, estaba perdiendo su entusiasmo por la revolución. En respuesta al ataque total de la organización de mantenimiento del orden SSC, la chica mágica Anarchy que lo anhela quema el cielo de Akihabara con un atractivo que amenaza su vida. ¡Para recuperar a la chica mágica cautiva Blue, el Ejército Revolucionario lanza un ataque contra la fortaleza de la prisión 'Big Sight'!

Joined by Pink, the three Magical Girls are now reunited. While Otaku Hero and the girls hold a rally at a maid café in Akihabara, one of SSC's Four Heavenly Kings launches a giant robot to face them in battle. What is behind Unit-@'s hatred of otaku?

After Otaku Hero loses a beloved toy robot in the Kanda River, he and the girls are confronted by the hostile middle-aged members of the Mansei Bridge Otaku Commune. The two generations enter a contest to fight over the true definition of otaku culture.

Otaku Hero takes the girls behind enemy lines in Shibuya to find an elderly collector with a drug that amplifies magical powers. The collector agrees to provide the drug in exchange for a rare figurine set locked away in the SSC base at Nakano Sunplaza.

With Otaku Hero and the girls in Nakano, SSC launches an attack on the Akiba Liberated Zone. The other otaku struggle to defend their base. On the way back to Akiba, Otaku Hero recalls his past with the magical girls and his first encounter with Shobon.

On their way back to Akiba, Otaku Hero and the girls are confronted by two of SSC’s Four Heavenly Kings—Adam and Eve. They get trapped in a cyberspace where Otaku Hero and Anarchy must defend against relentless attacks and cheats to rescue Blue and Pink.

Otaku Hero, Nick, and the other otakus get together to discuss the planning for the upcoming Wanku event. From merch, to guests, and even a possible physical media release, it's all on the shoulders of the appointed lead producer, Otaku Hero.

SSC forces attack the otaku at the Wanku! event with an army led by two of the Four Heavenly Kings—the silent Himawari and her overbearing older brother. Pink and Blue have to take the power-up drugs from Chogo-shi to defend against the deadly siblings.

With the thought of Anarchy's return casting a shadow over the otaku army, Otaku Hero rallies the troops and prepares for one final battle. Otaku Hero leads a direct attack on SSC headquarters while the magical girls stay to defend Akiba from Slayer.

The notebook that Otaku Hero found in the SSC base explains the origin of Shobon's hatred for otaku and foreshadows a dangerous fate for the magical girls. Running through the empty streets of Tokyo, Otaku Hero races back to try to change the script.

Once Slayer's blood transforms the magical girls into Magical Destroyers, Shobon moves his story toward its planned climax. There is little Otaku Hero can do to resist. What will be the fate of the otaku army and otaku culture in SSC's planned New World?