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The game's premise revolves around a high school student named Takumi Nishijō who unknowingly walks into the scene of a gruesome murder on his way home. More mysterious events start happening afterwards as more gruesome murders occur in the area. Takumi struggles to cope with reality and the delusions he experiences as he tries to avoid getting caught by the perpetrator behind the chain of murders.

The gameplay of Chaos;Head, like other visual novels, requires little player interaction as the game is primarily made up of text dialogues. The player only needs to read and click through the text to advance through the game. The text that is displayed on the screen depicts conversations between different characters or their thoughts.
Chaos;Head presents choices to the player through a unique "delusional trigger" (妄想トリガー mōsō torigā?) system.[10] This system presents the player with three choices relating to Takumi's psychological state. Two cardiac cycles will be displayed on the screen. A green, stable one will be on the top left hand corner and a red, unstable one will be on the top right hand corner. The third choice is not visible to the player as it requires no player interaction. The player may choose to click on the green or red cardiac cycle, or to simply proceed through the game without selecting either of them. The player is not required to make a choice immediately as the two cardiac cycles will remain on the screen until a predetermined number of lines has been passed since they appeared.
Selecting the cardiac cycles will often decide what kind of delusions Takumi will experience. The stable choice often shows a happy or humorous scene whereas the unstable choice will show very negative scenes possibly with gore and violence added. Yes and no questions also show up at times although they are much less frequent than the delusional triggers.