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.

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.

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.

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.

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.

In a closed meeting with Councilor Ogata, Superintendent Ibuki discloses to her superior that Ranmaru is a possible symbiote, telling him that she'll have him killed if it has to be the case. Later on, Ibuki informs Kureha to see if Ranmaru has the symbiote inside of him. Back in the TOKKO office, it was business as usual until Muramasa informs Ranmaru to entertain Kunikida, who didn't go to work since he was pissed off at the NPA officials for denying his search warrant on the forensic building. Ranmaru was about to tell Kunikida what happened at the forensic building last night when Kureha arrived on her motorbike. The two went out to visit a carnival and a cemetery, laying a flower on two graves. Kureha tells Ranmaru that the graves belong to her parents and her younger brother, who were killed in the aftermath of the Machida massacre.

Sakura relieves her memories of meeting with Inukai and her sister prior to joining TOKKO. After TOKKO's clash against Gaki demons, Ranmaru receives an anoynymous call from a mysterious person who could provide him information as to the true reasons behind the events behind the Machida massacre years ago. During his investigation, he is suddenly attacked by a lone Phantom demon in the nearby park, specifically the 13th Phantom demon. Later on, he is saved by Sakura and her TOKKO comrade, Inukai when the two killed the 13th Phantom. In a conversation between Ranmaru and Sakura, she warns him not to continue getting involved in fighting the demons anymore. Ranmaru is left baffled by her strange warning. Sakura is left to believe, at first, that some people in the Public Security Investigation Agency were responsible for Ranmaru's appearance in the park

As Ranmaru continues to get deeper and deeper into the mystery of the Phantom demons, he is accosted by two strange men wearing shades and wielding pistols when he was strolling in a local park. To make things worse, Saya gets injured in a depicted hit and run accident staged during her break hours by an unknown vehicle. Ryoko and the others inform Ranmaru that a secret sort of cult society may have hired assassins to kill her when the TOKKO unit met Ranmaru in the old Machida apartment. In the subsequent fight, Akiha helps Rannmaru awaken his bond with his symbiote demon by stabbing him in the chest before pushing him into the open hole that he (and the other TOKKO members have seen 5 years ago) had seen in the Machida massacre. Ranmaru's awakened symbiote soon turned the tides in the favor of TOKKO when his symbiote defeated the demons in the area.

Ranmaru gets unofficially transferred to the TOKKO division while still being under the official command of TOKKI, which pissed off Kunikida and thinks that Akiha may have been responsible for Ranmaru's supposed transfer. In a meeting with the Phantom Countermeasures Committee, lead by top NPA (and possibly Public Security Investigation Agency) officials, they accuse Ryoko of wasting her time in their investigation against the Phantoms and not doing anything to calm the public about the supposed serial murder cases since Ranmaru's own symbiote was awakened by her subordinates without enacting on their authorization. In the dead of night, Gaki Phantoms infiltrate a NPA office in Tokyo in order to assassinate Ryoko in order to halt TOKKO's investigation against them. In the subsequent fight, Ryoko gets minor injuries on her left arm and they discover Ranmaru's power, which was the ability to channel his symbiote energy on his broadsword to do a projectile attack.

Yukino visited Ranmaru in the Shibuya Police Station in the early morning, delivering the book regarding the Box of Dirge and information regarding a supposed piece of the box. During a courtesy call to an old man who have called Ranmaru earlier on, his symbiote was slowly corrupting his mind and body after his attacks were thwarted by his mysterious strength. He was rescued by Sakura and the others with an unknown necklace on his neck, but Ranmaru's slowly corrupted symbiote used him to attack Akiha and the others before Ryoko was forced to use her Colt SAA revolver to fire a shot at Ranmaru's chest, mortally wounding him. Sakura decides to enter his dreams by stabbing the both of them with her sword, rendering her unconscious also. When Sakura attempted to rescue Ranmaru to bring him back alive from the vision of his late parents, his corrupt persona slashed at her chest with Ranmaru's own sword, nearly making her status critical.

Hiroki, Sakura's younger brother, was awakened with a Phantom spirit when it infiltrated the Udagawa Police Hospital in Tokyo and doctors who were attending to the unconscious teenager. During an encounter with TOKKO, Hiroko wounded Sakura and drove off the other members, barely surviving. Despite this, Sakura wishes to help her brother by trying her best to purge the Phantom spirit out of his body and does not wish to kill him. Later on, Ranmaru and Sakura head off to Machida to look for clues at the old apartment complex when Hiroki reappeared with Gaki Phantoms along. TOKKO had its first casualy when Inukai sacrificed himself, killing Hiroki by cutting him in half, but not before he too had the same fate. It was revealed that Taishi, the man whom Ranmaru visited a day ago, was the one mostly likely responsible for implanting Hiroki's Phantom spirit inside him.

TOKKO had decided to move Saya to a safer place, more specially Ryoko's apartment instead of the Shindo's for her own protection. During Ryoko's surprise visit, she managed to obtain information from Muramasa that he was the inside man paid by Taishi to provide police information regarding the case after threatening him with Ryoko's Colt SAA revolver. Later on, Taishi dispatches Gakis to assassinate all active TOKKO members as a means of further slowing down their investigation against him. Surviving the said incident with help from the Araragi siblings, Ryoko obtains an arrest warrant for Taishi. Despite heavy security, the group was able to penetrate deep into Taishi's mansion, but not before he escaped.

Kunikida encounters Muramasa and after an argument, the two tried to shoot each other out when the former heard Muramasa ordering Shindo and the other TOKKO operatives to be arrested and taken care of when PSIA agents tried to raid Ryoko's apartment to arrest Shindo, Sakura and Kureha with Kunikida shocked to realize that Muramasa is a PSIA agent in reality. Kureha and Sakura stormed the supposedly empty PSIA complex to rescue Ryoko with Gaki Phantoms, which had appeared due to low security. In a change of heart, Kunikida assists the two TOKKO agents by breaking Ryoko out of her cell, only to be arrested by PSIA agents for helping Ryoko escape. Back at the Machida apartment complex, Shindo and the others assemble to do battle against Taishi, with Kureha severely wounded. Ranmaru and Sakura head into the underworld via the giant hole in order to rescue Saya and defeat Taishi.