Ranmaru Shindo, five years after surviving the tragic Machida massacre, graduates from the Special Mobile Investigation Troops First Division training academy after he was recruited into the police force as a patrolman since the two Shindo siblings have joined the police force as part of moving on from what happened in Machida. During his transfer to the Shibuya precient, he encounters the red-haired woman in a police uniform who had been the sole cause of his nightmares and two officers, who are said to be elite officers from the TOKKO division. Ranmaru, with his friend and partner Ichiro Hanazono, investigate their first case of homicide with their superior Kaoru Kunikida after being indoctrinated into TOKKI when mysterious people began to attack the investigation team and their patrolman escorts with brute strength. It appeared that their sheer strength was about to defeat them for good. Ranmaru thought that he was about to die on his first day of duty as a TOKKI detective when the red-haired girl, wearing a black jacket and wielding a broadsword, arrives in time to battle the strange men and in fact, decapitates one of them holding Ranmaru by his throat

Being cornered by strange men with brute strength, Ranmaru and Ichiro were about to be killed when the same red-haired girl and her comrades rush in to save them by killing the suspects with their swords and daggers. They reveal themselves to be from the TOKKO division after they eliminate the strange-looking larvae from the decapitated bodies and their forensic teams arrived. The red-haired woman hints to Ranmaru that she was one of the former tenants from the same apartment building where the Shindo siblings once lived in. During an investigation done by Kunikida and his colleague, Shogo Muramasa, on what earlier, they discover that the Machida massacre may have been covered up by those from TOKKO and by the Public Security Investigation Agency (PSIA), citing undocumented reports of a demonic killer in one of the strange incidents in Kameida. Later on, the TOKKI detectives are forced to confront the demon-controlled suspects again to no avail, only for the TOKKO division arrive in time to kill them once again in Miyashita Park. During an investigation on Ranmaru's old neighborhood, he realizes that the red-haired girl was his ex-neighbor Sakura Rokujo

With the recent attacks on police officers by the possessed human-like zombies and Ranmaru's near fatal death from one of them a few days ago, he began to reflect about what happened from his first day of duty as a TOKKO detective and on the Machida massacre, especially on the mysterious tattoo that appeared on his right arm. Concerned about where it came from and how it showed up, Saya took him to a nearby police hospital to be checked up on. While waiting for the results of his checkup, Ranmaru sneaks inside a PSIA-guarded hospital ward that housed Sakura's younger brother, who was almost a victim in the Machida incident. Later on, Phantom-controlled larvas infiltrated the hospital and possessed some of the hospital's medical personnel to assassinate Saya. Even though Ranmaru tried to protect her by firing her revolver on the possessed humans, Sakura came to the rescue and killed them. The incident had promptly forced the police to seal off the entire building and cover the entire incident by blaming it on insane patients inside the hospital. In order to take their minds off from the assassination attempt, Ranmaru and Saya went out on for dinner, only to find their boss Kunikida as an uninvited guest.

Saya gets Ranmaru a date, in the form of forensic expert Yukino Shiraishi, who happens to be Saya's upperclassman in her high school days. During Ranmaru and Yukino's date, Ranmaru discovered that the demons who were responsible for the Machida massacre five years ago and for the death of his police comrades were believed to be of European origin, with Yukino filling Ranmaru in on the background on a Western urban legend that the demons were summoned by alchemists in order to achieve immortality during the Middle Ages in Europe. Ranmaru was horrified that the pictures in a book found in southern Italy were the same ones that he had encountered a few weeks ago. During a conversation with Saya, she told Ranmaru that Yukino's late mother was murdered supposedly by a vicious thief. Thinking that Yukino may be in danger since her mother's death was at the time when the Machida massacre took place at the same time, he went back to the forensics building to check on Yukino when a Phantom humanoid appeared in the dark and tried to attack Ranmaru, but a spiritual barrier appeared out of nowhere and dazed the human larvae, forcing the humanoid to fight Ranmaru himself. He was eventually wounded by Sakura's broadsword, making the humanoid retreat in defeat with an arm cut off from it.

Covering the incident of Ranmaru involving a car accident as a cover story, Ranmaru encounters Saya in his hospital room. She warned him not to get further involved into what had happened to him near the forensic building last night. Kunikida, thought to have granted a request to investigate the forensic building for evidence to suggest that TOKKO was concealing evidence from the public, which was denied by top National Police Agency officials. Yukino then visited Ranmaru back in the Shibuya police station, warning him that her father was researching on the strange creatures that Ranmaru had encountered before. Wanting to quell his suspicions, he requests a meeting with Dr. Shirashi, who fills him on the legend of the Box of Dirge, the artifact that the alchemists used in the Middle Ages to connect the human world with the underworld, only that demons were summoned from the box. Ranmaru found out that the Box of Dirge broke into 108 pieces, living inside each Phantom demon. The story made Ranmaru even more suspicious of Dr. Shirashi and when he entered the abandoned Special Organisms Laboratory, only to discover that the chief researcher himself had consumed parts of the demon hand that police found near the scene of the Machida massacre, turning him and his research staff into half-human/demon hybrids. Before the mad Dr. Shirashi could kill Ranmaru, Yukino was critically wounded when she interfered by blocking Dr. Shirashi's attacks on Ranmaru. The mad scientist tried to escape, only to be killed by two unknown people (known as the Araragi siblings in the manga). Kureha and Sakura raid the forensic building to secure Ranmaru from harm, killing the half-human/demon hybrids instead.