Ichiro Onizuka and Saki Toyama continue their work solving cases at the Shinjuku Higashi Police Station, but the arrival of a strict new chief, Kanata Azuma, threatens their operations. Opposing Onizuka's unconventional methods and constantly clashing with Keitaro Jin over investigation policies, Azuma brings a tense, disruptive friction to the Criminal Division.
The body of a man named Yugo Matsumoto is discovered, prompting Onizuka to recall a report the victim had previously filed regarding a stolen motorcycle. As Onizuka, Keitaro, and Saki investigate a potential connection between the theft and the murder, their efforts are immediately hindered by the station's strict new police chief, Kanata Azuma, who disapproves of their methods.
When a body covered head to toe in strawberries is discovered at the Shinjuku Botanical Garden, the investigation stalls over the unidentified victim and the unusual fruit. Onizuka eventually identifies the deceased as Eita Takanabe, a co-developer of the garden's early-harvest strawberries, but suspects that the employee who first found the body is hiding a dark secret.
When a cybercrime assistant inspector is poisoned in Shinjuku Ni-chome, a simultaneous power outage strikes the station due to a system failure in the "Shinjuku I-City" smart city project. Onizuka soon discovers that the murdered inspector had been conducting a rogue investigation into a cyberattack targeting one of the project's tech companies.
Following the poisoning of two cybercrime investigators, a devastating virus spreads rapidly through the computers of companies involved in the "Shinjuku I-City" project. While Police Chief Kanata Azuma begins exhibiting highly suspicious behavior, Onizuka meticulously sifts through Shinjuku's security footage and notices a unique, moving landmark that holds the key to unmasking the invisible killer.
While heading home, Onizuka is attacked with a stun gun by an unknown assailant whom he recognizes as Yukio Kasai, a convict from a murder case he handled ten years prior. Partnering with the original lead investigator from the Shibuya Kita Police Station, Onizuka dives into the newly released convict's background, ultimately uncovering a tragic truth behind the assault.
When a horrific night bus crash bound for Shinjuku claims eleven lives, the driver's history of drowsy driving makes the incident seem like an accident. However, after reviewing the dashcam footage, Onizuka suspects foul play and raises the possibility of murder. The investigation intensifies when the team discovers a mysterious twelfth passenger was on board and has since gone missing.
Overcome by guilt after regaining consciousness, the bus driver attempts suicide in front of Onizuka, while the identity of the missing twelfth passenger remains a mystery. Using his precise memory of the area and its residents, Onizuka deduces that the true culprit is linked to a group of unfairly dismissed former employees from the bus company. Keitaro and his team launch a targeted investigation into these workers, racing to uncover a deeply tragic truth.