Following the incidents involving Burst Linker Dusk Taker, Kuroyukihime remembers bringing Haruyuki Arita into the "Brain Burst" program—a software that enables users to speed up their cognitive processes to the point where time appears to halt. Since joining, Haruyuki has gained recognition among other Burst Linkers and has assisted Kuroyukihime in her objective of attaining the top level within the game. In the midst of a territorial conflict with their legion, Nega Nebulus, Haruyuki and his companions are ejected from the program due to a catastrophic storm within the game. Security cameras across Tokyo begin to fail, a phenomenon Kuroyukihime concludes is connected to a Brain Burst malfunction. Resolved to resolve the crisis, Nega Nebulus needs to enlist other legions to locate the cause of the glitch and bring back the acceleration function.