Two months following the resolution of the serial murders in Inaba, Yuu Narukami returns to the sleepy town to reunite with his old friends. However, he is not prepared for the Midnight Channel to reappear again, prompting the reformation of the Investigation Team to find out why. At the same time, a flight bound for Kagoshima is hijacked before takeoff, with the perpetrators making off with specialized cargo. Determined to retrieve what was stolen, Mitsuru Kirijo and her partner Aigis chase after the criminals to Inaba.

While kicking off their investigation, Yuu finds that he is unable to reach some of his friends since the appearance of the channel. Believing that they have been pulled into the world within the TV, the Investigation Team dive in to search for them, only to reawaken in their high school and be forced into a battle tournament called the P-1 Grand Prix. The separated members must fight their way through the school against each other's alternate versions if they want to uncover the mystery behind their friends' disappearances.

Meanwhile, Mitsuru and Aigis' search for the missing cargo also leads them into the world within the TV. Trapped with no means of escaping, the Shadow Operatives must navigate through the same competition to find what was taken from them.

[Written by MAL Rewrite]