Superintendent Ryōko Yakushiji and her subordinate, Assistant Inspector Junichirō Izumida of the Tokyo Metropolitan Police Department, launch an investigation after they witness a man combust somewhere in Ginza. The two officers learn that the combustion cases may be tied with a known religious cult, but Ryōko has to endure her rivalry with fellow superintendent Yukiko Muromachi and an assassin out to get her.

Ryōko barely survives an assassination attempt with the assassin sacrificing herself by ingesting a suicide pill that made her combust. She and Izumida continue to investigate, with their case getting complicated when a forensics scientist the two officers knew for a long time is the leader of the cult and that they had been using growth hormones to make an ordinary snake grow large.

Two newspaper reporters try to follow Ryōko and Izumida around to get a potential story to be used against the former, but are seemingly thwarted in their plans when JACES security forces intervene on Ryōko's behalf after following the two for some time.

Ryōko and Izumida investigate a former Minister of Health, Labour and Welfare due to illegal human experimentation of human cells with cells from an unknown species, which resulted in a monster-like infant. The two officers try to eliminate the creature before they decided to let it die due to rapid cell degeneration.

An anti-terrorist security robot goes haywire after a traffic accident and kills armed security guards. Ryōko and Izumida are drawn to the situation after the former claimed of hearing gunshots. The situation becomes complicated when Izumida's elementary school cousin Mana gets involved and armed tactical teams of the Japan Private Police (JPP), a JACES rival and a known PMC-type security company, are secretly deployed to destroy their own invention and conceal evidence on the victims the robot had killed.

Marianne and Lucienne, Ryoko's maids, arrived in Narita International Airport after the two subdued a thief by kicking their baggage cart to knock him out. The two maids, with Ryoko and Izumida, investigate the appearance of a giant salamander beneath the Greater Tokyo Area within a secret underground resort used by corrupt politicians who send gunmen to kill the creature.

Ryoko and Junichiro head to Okinawa to investigate the reclusive JPP founder Ryojin Tadomura. As the two begin their stay in the island, seeds from mutant mangrove trees that were experimented on by JPP scientists turned JPP personnel against other humans until the mutated mangrove in the destroyed Tadomura villa is destroyed by Marianne by napalm.

When numerous people are committing suicide, including a well-known police forensics scientist, Ryoko and Izumida investigate it and find out that a university professor and a new species of ultrasound crickets are responsible for the mysterious suicides.

Ryoko goes into hiding after the media broadcasts negative articles and news reports about her fame and her standing with the Tokyo Metropolitan Police Department. Ryoko takes Izumida to a JPP stronghold in the Greater Tokyo Area after being defamed by a secret organization of renegade police officials led by a woman named Ruriko Isurugi. In the JPP stronghold, Ryoko and Izumida discover a child who has the identical facial features like the Ryoko.

Ryoko and Izumida find out that the child had no memories of herself, dubbing her Monami. Meanwhile, Ruriko makes an alliance with the Defense Minister on taking on Ryoko after reports of explosions have hit the DK Pharmaceuticals and other public buildings. Distraught over Ryoko planning on keeping her out of Japan, Monami runs away only to be captured by JPP operatives in an ambush with centipede robots until a giant toad came out of a nearby lake and assisted Izumida.

Monami seeks refuge with Izumida after escaping from captivity. Ryoko reveals that Ruriko had co-founded JACES as the Japanese Empire Security Service but left after her grandfather Masamoto refused to allow Ruriko to use JESS as a refuge for ex-Imperial military servicemen to reestablish a new Japanese military. Izumida learns from Kazuma, Ryoko's personal assistant, that Monami was cloned to wrestle control of JACES away from the Yakushiji family using a combination of ancient technique of making people called Hangon and cloning technology.

Ruriko and other conspirators in the JGSDF and the JPP had planned to crush Ryoko Yakushiji and JACES under the guise of anti-terrorist exercise for the Greater Tokyo Area. Ryoko decides to fight Shiba on her own with JPP forces attacking both her and her subordinates. Izumida leaves the Yakushiji residence to see Ryoko, who had been previously attacked by an AH-64 Apache and a Type 90 MBT when a Type 10 tank arrives in a harbor to finish off Ryoko for good.

The Type 10, revealed to be under the control of Marianne and Lucienne, is used by Ryoko and Junichiro to head to Central Tokyo as they take out renegade JGSDF Type 90s. They later proceed to take out Tokyo Tower with Type 81 Surface-to-air Missile, which is the source of the radiowaves that had been used to mind-control JGSDF soldiers. Monami was rescued by Ryoko and Junichiro after defeating Ruriko and Kazuma. With the mind-control signal removed, the JGSDF personnel involved in the plot collapsed and the remaining JPP operatives fled in fear due to the destruction of Tokyo Tower. The actions of Ryoko and her group were credited in the media as various training accidents.