Ichiro Onizuka is a skilled detective who is confined to a wheelchair after being injured in an incident that occurred right before his retirement. Armed with a detailed "city of memory" in his mind, he solves modern-day cases while recalling the cases of the past.
When a fatal explosion destroys a local pyrotechnic factory, Onizuka connects the deceased president to a past assault involving a predatory finance company. While investigating the factory's massive debt alongside Saki, Keitaro, and new teammate Yojo, a second explosion kills a disgruntled former worker who leaves behind a digital suicide note confessing to the initial bombing. Although the police force prepares to close the case as a murder-suicide, Onizuka uncovers hidden evidence that upends the entire investigation.
Three years after turning himself in for his mother's murder, a man still refuses to reveal where her body is hidden. Based on Onizuka's deductions, the team canvasses Shinjuku and uncovers a dysfunctional family dynamic involving pension fraud and severe caregiver burnout. To crack the suspect's stubborn silence, Onizuka connects the case to an unusual mass death of civets that occurred in the neighborhood three years ago.
A man harboring a deep grudge attacks Saki, blaming her for ignoring his harassment complaint five years ago and claiming his girlfriend is now being held captive by the same stalker. Saki and Onizuka rush to investigate, but the accused suspect denies everything, and the case spirals into a web of lies when the girlfriend's drowned body is discovered in the Ichigaya Moat. With multiple suspects emerging and a mysterious herb shop tied to the crime, Saki must overcome her past regrets to uncover the truth.
Just as Saki shocks the team by submitting her resignation, Yojo's close friend is found murdered near a controversial, illegally constructed apartment building. Onizuka joins the task force to investigate and discovers the victim had been using a group chat app to vent about his real estate job. The case takes a deeply personal turn when one of the group chat members flees upon seeing Onizuka, exposing an unexpected link to the detective's own past.
While Saki takes a leave of absence to contemplate her future, a random assault in Nishi-Waseda escalates when the suspect steals an officer's patrol bicycle and flees. Social media tracking reveals the fugitive is Saeki, but Chief Inspector Mori fiercely opposes Onizuka's involvement in the manhunt. The crisis deepens when the officer who lost his bicycle goes missing and gunshots ring out through Shinjuku, forcing a benched Saki to grapple with her choice to leave the force.
After a missing officer's body is discovered in a Nishi-Waseda pond, the arrested suspect confesses to murder but claims his original target was Onizuka. Sensing a contradiction between the suspect's story and the deceased officer's combat training, Onizuka overrides fierce objections from Chief Inspector Mori to launch a rogue investigation. Joined by Keitaro, Saki, Yojo, Junko, and Kurita, Onizuka uncovers a specific phrase in the police log that triggers his memory and exposes the true motive behind the tragedy.
When the chairman of a delivery company is found murdered and covered in a unique blueberry sauce, Onizuka traces the ingredient to a regular customer named Kinjo. Investigating Shinjuku's Golden Gai, the team discovers that the victim was a former police officer who shared a hidden history with Kinjo, a former student activist. As a pivotal 1968 Shinjuku incident flashes through Onizuka's mind, he races to unmask the killer while Saki finally finds the answer to why she wants to be a detective.