Haruyuki defeated Legendary Class Enemy Archangel Metatron. There was very little time left before the body of the ISS kit that infected the Accelerated World was destroyed... but Black Vice and Argon Ares from the Acceleration Research Society suddenly appeared and kidnapped the Red Queen Scarlet Rain.

Having promised to protect Niko Haruyuki, he receives help from the one freed from Metatron's shackles and sets off in pursuit of Black Vice.

At the same time, Kuroyukihime, along with Fuko, Utai and Akira, go to the Midtown Tower portal to disconnect Niko from the real world...