Shuuichi Inaba is a student of a special high school for young prodigies and one of the users of the newest and most popular application called 'Alice in Cyberland' - an app with an AI that enables its users to talk to them as with any other human. When some of the students of his high school start to get attacked by a mysterious culprit, Shuuichi is determined to find out who it is. In his investigation, he stumbles upon 'Alice' - a special kind of program, which, in return for helping him with the case, demands only to know something he would usually never tell anyone - his biggest and deepest secret.

From MangaHelpers:
After his father died, Naruse Akira retreated into video games, and his mother retreated into alcohol. Naruse plays games almost all the time, getting him in trouble at his private school and worrying his childhood friend Hoju. He's incredibly good at war games because he is good at reading his opponents.
One day, he ends up downloading a strange game called "Revolt" onto his phone. It's a game that has him orchestrate a revolution, and the graphics seem incredibly life-like. At the end, he learns that he was actually giving real-world orders, and that the game was part of a scouting process for a company that helps to run revolutions. Now they want him to be their commander and help them save the world.