Some time after the events involving Burst Linker Dusk Taker, Kuroyukihime recalls recruiting Haruyuki Arita to the "Brain Burst" program—an application that allows players to accelerate their cognitive functions until time seems to stop. Since his arrival, Haruyuki has risen to fame among the other Burst Linkers and has been helping Kuroyukihime achieve her goal of reaching the highest level in the game.

During a territorial battle with their legion, Nega Nebulus, Haruyuki and his friends are kicked out of the program after a destructive storm in-game. All over Tokyo, security cameras are malfunctioning, which Kuroyukihime deduces is related to the Brain Burst glitch. Determined to fix the problem, Nega Nebulus must recruit the other legions to find the source of the issue and restore the acceleration ability.