The story of 12Riven takes place on May 20, 2012 with Renmaru Miyabidō biking his way speedily towards the abandoned Integral (インテグラル Integuraru) building after receiving a message on his cellphone that Myū, an old friend of his, would die at the building's top level today at noon. When he gets there, he checks his wristwatch and sees that it is 11:24 AM.
Elsewhere, Narumi Mishima is on her motorcycle heading towards the same location. She has received a request from a friend and coworker asking her to help save a girl named "Myū" at Integral. Narumi must save Myū to prevent the execution of the "Second Eclipse Plan" (第弐エクリプス計画 Daini Ekuripusu Keikaku). Narumi has never heard of this phrase before, moreover, the message was sent with the "XXX Lv6" marking. This was a rating scale for the severity of a situation and a level 6 marking has never been used. Even a large scale terrorist threat was set at level 5. The message also indicated to Narumi that someone named Renmaru may be there, that he will be on her side.
Renmaru finds nothing at the observation deck of the building, but when he goes outside onto the opening of the building, he finds Myū injured on the ground. Renmaru also finds her attacker there but is unable to defeat him because every time Renmaru tries to connect a blow, he is thrown onto the ground himself by some unknown force. At this point, Myū's attacker draws out a gun, he takes Myū and threatens Renmaru to leave the place quietly after he counts to ten with his eyes closed. Renmaru does not know what to do and stands there hopelessly. Right as the attacker counts down to one, Narumi arrives at the scene and points her gun at him.