Chaos;Head's story is set in the year of 2008 in Shibuya and is centered around Takumi Nishijou, a high school student at the private Suimei Academy, and some strange events that have occurred recently in the Shibuya area. Two events have occurred so far and is being referenced by the media and the public at large as being New Generation events. The first event named "Group Dive" occurred on September 7th with five high school students jumping to their deaths off of a high tower. The second event occurred on September 19th wherein a male was found dead with a thirty-two week old fetus incised within his abdomen.

The story begins on September 28th with Takumi talking to an online friend named Grim. Grim has to provide Takumi with the background about the recent New Generation events since Takumi is not interested local or international news. A person named Shōgun joins the chatroom though he does not say a word until Grim has left the chatroom. Shōgun confronts Takumi and presents him with a barrage of image links that depicts a very gruesome murder.

The next day, as Takumi was heading home after spending the afternoon at an Internet cafe, he comes across the same scene that he witnessed yesterday in Shōgun's pictures. He runs away from the crime scene screaming, but not before meeting a pink-haired girl there covered in blood and wearing Suimei Academy's uniform.

The story progresses from here with Takumi trying to avoid getting involved with Shōgun and other New Generation events as he is slowly caught in a grander scheme's wheels of motion.