During the Middle Ages, a wealthy family had a puzzle box created in order to gain immortality, not knowing that it would in fact open a portal to the demon world. 108 demons were unleashed, shattering the device into 108 fragments which they then absorbed. Once extracted from demons and reassembled, the 108 fragments can be used to close the demon's portal, which if allowed to grow will result in the destruction of all humans on Earth.

A young man named Ranmaru Shindo lives with his younger sister. They moved from Machida (a city located in the western part of Tokyo’s greater metropolis) 5 years earlier, after the massacre of their parents in their apartment complex, which was attacked and overrun by unknown assailants who ruthlessly and brutally killed almost everyone in several buildings in the complex. He has also been having recurring dreams of a girl for some time, but they are growing more frequent. She seems to be covered in blood holding a giant sword. But in reality, someone used the puzzle box to create a portal to the demon near the Machida apartment complex, whence came the demons who killed most of the residents.

At the beginning of the tale, Ranmaru graduates from his cadet class to become a new investigator for The Special Mobile Investigation Troops First Division or TOKKI to avenge his parents' death. Later on the day of his graduation, he sees the girl from his dream wearing a police uniform. She is a member of Section 2, known officially as Special Public Safety Task Force, or Tokko for short, being under the eye of the Public Security Intelligence Agency. Throughout the story, it is explained that there are many rumors about Tokko, one of which is that they use swords to execute criminals and that body parts are often found at the crime scenes Tokko investigates. There are also rumors that they aren't even human.

All members of Section 2 bear a tattoo ( except for Ibuki who is not a symbiont). This is their "symbiont tattoo", which marks them as carriers of a "phantom", one of the 108 demons. Not all of the symbionts are with Section 2. A symbiont may be good or evil, but the spirit's alignment is unknown until it is awakened within the host. The tattoo also imparts a type of protection from other phantoms and expands after the phantom’s awakening. Only symbionts have the strength, speed and endurance to kill the demons with bladed weapons. Using the symbionts, Section 2 hunts down the other Phantoms, dismembering them to get the 108 fragments to close the Machida hole before it expands and the entire world is covered with Phantoms.