In the year 203X, a security robot goes on a rampage in Shibuya. Nakamura Nao, a police detective with the public safety department, commissions detective Akechi Kogorou to solve the case... but Akechi, along with Inoue Ryou of the Boy Detectives Club, is already heading toward Hinomoto Heavy Industries, the robot's manufacturer. Meanwhile, Hanasaki Kensuke of the Boy Detectives club is pursuing a lost dog after receiving a report from the club's technical whiz, Noro Makoto. As Hanasaki corners the dog in an abandoned building, he finds himself face-to-face with a mysterious boy...
A young woman approaches the Boy Detectives' Club and asks them to find the intended recipient of a series of threat letters her boyfriend made. They accept the job and begin to tail her boyfriend. Meanwhile Kobayashi, after missing his chance to return Hanasaki's dropped wallet, uses it to buy a desperately needed meal. Hanasaki finds out by checking his electronic money usage history, and he convinces Kobayashi to join him on the current investigation in a second attempt to get him to join the club...
Kobayashi somehow feels that maybe he can die if he stays with Hanasaki, so he joins the Boy Detectives' Club. His first mission is to help find a jobless young man who's gone missing. The club starts by receiving files on missing persons from Detective Nakamura and her subordinate, Miyanishi, who are facing an investigation of their own now after a medical examiner went missing. They were all set to begin the search, but when the mysterious and socially awkward Kobayashi perpetually clashes with Inoue and Noro, he tries to make a run for it.
After school, Inoue watches Katsuda of the tennis club practicing before heading home, and Hanasaki tests out some tools of the Boy Detectives' Club trade with Scientific Experiments Club members Ohtomo and Yamane. Meanwhile, a police car is found overturned after a crash. A film reel labeled "For Akechi-kun" is found in the car, and one of the passengers, Senior Officer Kanda, is missing. The film reel depicts Twenty Faces telling Akechi that if he can't find Kanda by 9:00 PM, the senior officer may lose his life...
Kobayashi and Inoue are trapped in the underground discharge channels as a result of Twenty Faces' maneuvering, and a massive amount of water is pouring into their chamber. Worried about the police officers searching elsewhere in the channels, Inoue tells Kobayashi to escape with the message that the map they were given is fake and they need to evacuate immediately. However, the officers still end up trapped. Hanasaki rushes to rescue them and talks the former Boy Detectives' Club member Katsuda into helping him get to the scene faster. But as they're en route, more and more water surrounds Inoue...
Hanasaki has been trying various things to help Kobayashi die, but nothing has worked. Then, while Akechi is away, Hanasaki takes the liberty of accepting six job requests. He's noticed that all the times Kobayashi has been injured were after completing a job, so he thinks that if they complete lots of jobs, his wish will come true... but things don't go exactly as he planned.
Akechi is relaxing at a spa to relieve the exhaustion of his recent cases. A story about the security robot incident, the organ-selling incident, and the underground waterway kidnapping incident come on the TV, discussing a "mysterious cooperant" who resolved them all... in other words, Akechi himself. Then Nakamura asks him about his history with Twenty Faces, and Akechi begins to recount the trauma of his youth. Meanwhile, Hanasaki also carries the weight of a checkered past, as he's summoned home by his father.
The residents of the Kokorogaoka Housing Complex refuse to vacate their homes for the sake of urban development, so they declare its independence from Japan as an autonomous borough. The one to make this announcement is none other than Hanasaki's older brother, who ran away from home years ago. Hanasaki asks Akechi for help, but Akechi refuses to do any job he hasn't been hired for and confines Hanasaki to the building. Then a mysterious package arrives, and its contents reveal that Twenty Faces was the one behind these current events. Unable to wait around, Hanasaki heads for the housing complex himself...
Kensuke is bewildered when Haruhiko invites him to live together, but Isuzu is negotiating with the police for three billion yen in exchange for the removal of the residents of the housing complex. Meanwhile, Nakamura requests the aid of Akechi and the Boy Detectives' Club in the case.
Hanasaki runs out of the office after an argument with Akechi and the others, only to end up confined by Twenty Faces and shown several video clips: Haruhiko in the hospital after surviving the gunshot, a girl who died when she didn't receive a needed organ transplant from the facility that the Boy Detectives' Club shut down, Hanasaki's father at a press conference for the opening of his new commercial complex... and finally, the rest of the Boy Detectives' Club carrying on without him. These videos and Twenty Faces' words cut deeply into Hanasaki's psyche.
Hanasaki's act is successful in convincing Akechi and the Boy Detectives' Club that he was kidnapped by Twenty Faces. Akechi takes off to try to save him, saying he has an idea where Hanasaki might be. Kobayashi and the others are left behind, but Ohtomo gives them a hint as to where Akechi's gone, so they set out to track him down. Hanasaki is at Le Waqua, following Twenty Faces' instructions to take over the complex by controlling its security robots. Then Akechi arrives, and an epic shoot-out with the security robots unfolds.
Even with a gun pointed at him, Hanasaki is brought to tears by the conversation between Twenty Faces and Akechi. Then the Boy Detectives' Club arrives on the scene. Inoue and Katsuda try to rescue the employees being held hostage by the security robots, while Noro and Ohtomo struggle to stop the robots. Kobayashi is stricken by an impulse he's never felt before and runs toward Hanasaki, but Twenty Faces had already seen all this coming and brainwashed the employees to turn on Inoue and Katsuda. He then declares that if Akechi kills Hanasaki, he'll make the employees stop and the whole thing will end.
With the Le Waqua incident resolved and Twenty Faces in custody, the world appeared to be at peace again. However, the trauma of the incident left Hanasaki psychologically unstable, and the Boy Detectives' Club is reluctant to let him return to the ranks. Meanwhile, Inoue and the others are approached by Police Detective Miyanishi with a request to catch whoever is responsible for uploading candid photos of celebrities to a website called "Lynch Shot" without permission. The investigation begins, but Kobayashi can't help worrying about Hanasaki.
Yamane Tasuku, a younger member of the Scientific Experiments Club alongside Ohtomo, is troubled by three things. The first is that Ohtomo picks on him too much. The second is that he's always left behind in conversations. The third and most troubling of all is that he doesn't know how to become a member of the Boy Detectives' Club. One day Yumeko approaches him, mistaking him for a member of the club and asking him to investigate a case in which the school's most attractive boys are becoming victims of theft. But Yamane is so pleased by the mistake that he accepts the job...
After being out of touch for so long, Akechi calls the office. Kobayashi complains to him that Hanasaki is acting weird, and Akechi tells him, "do to him what he did to you." Then the Boy Detectives' Club receives an odd request: a death-row prisoner who's received a death threat has asked specifically for them to guard him when he's escorted to the district court. Inoue is reluctant, but Kobayashi, thinking that solving this case with Hanasaki will restore things to the way they were, accepts the job for them.
To escape the enemies targeting Fukiya, the death row prisoner they're guarding, the Boy Detectives' Club takes refuge in the abandoned building that Kobayashi had once been using as his base. They manage to hold their ground as they wait for a helicopter sent by Noro. In the meantime, Kobayashi has no choice but to play along with Fukiya's word association game, which causes his mental state to grow increasingly unstable. Meanwhile Hanasaki, after being accepted into Hide-chan's Red Beetle gang, learns of their involvement in the case and has to make a choice...
Kobayashi is in extreme pain after taking a gunshot.Has the mysterious power that protected him disappeared? Inoue is stunned by Akechi's prediction. Perhaps Kobayashi actually wants to live? Hanasaki is shaken at the sight of Kobayashi at death's door. Akechi gives advice on how to save him, but then reminds him that he was the one who made Kobayashi want to live, and tells him to do something about the situation himself before making another shocking declaration...
Inoue and the other detectives are disheartened after being told that the Boy Detectives' Club would be disbanded. The strange air around Kobayashi has returned and is working hard to heal his wound. Around the same time, Akechi is recalling his past with Twenty Faces. During a time of war, when Akechi was a mercenary, he and Twenty Faces came through many vicious battles together... but he was growing bored of the thrills that Twenty Faces arranged for him. Then he met Fumiyo, a Japanese reporter, and the two of them were increasingly drawn to each other...
As he's resting to recover from his gunshot wound, Kobayashi has an odd dream in which he sees a woman in a bed and a man approaching her. He doesn't recognize them, but the dream gives him a strange headache. Meanwhile, Hide-chan makes contact with Hanasaki, inviting him to help them punish someone who's been posting damaging information online under a pseudonym. But Hanasaki refuses, so Hide-chan leaves, saying there's too much to do and not enough time. His words make Hanasaki think about what it is he wants to do, and he sets off to visit Kobayashi...
Kobayashi, along with Inoue, searches for the place that he saw in his dream. Hanasaki and Hide-chan then show up and offer to help. Shortly after, Kobayashi has a flashback after seeing gingko trees lining their path, then takes off running toward an abandoned building. Meanwhile, the police catch Akechi on the security cameras breaking the fake Twenty Faces out of prison. The police suspect Akechi is the real Twenty Faces, but Miyanishi disagrees and sets out to find the truth alone.
Miyanishi was shot to death by Nakamura. During her interrogation, Nakamura testifies that Twenty Faces is actually Akechi. Determining that she may have been under his control, the police conduct a search of the Akechi Investigation Firm office. Hanasaki insists that Akechi can't be Twenty Faces, and Inoue demands proof, but the police ignore them, and the Boy Detectives' Club are reminded of their own powerlessness. Meanwhile Akechi, now on the run, suspects there's something more behind this incident and starts looking for the truth.
Akechi, stunned to learn that Nakamura was brainwashed by Twenty Faces, ends up captured by the special security force. Meanwhile, at the New Tokyo World Fair, the plane built to carry people to the stratosphere is involved in a catastrophic crash. The Boy Detectives' Club is at a loss, and their attempts to reach Akechi fail. Then, suddenly, Twenty Faces appears on their monitor...
The Boy Detectives' Club arrives at the Space Expo. Hanasaki and Kobayashi board the shuttle for the craft in the sky that Twenty Faces uses as his base, where Akechi is being held captive, but the shuttle is blown up and the two of them are held in place by security robots. Inoue and the others face off against the special security force, but they're at a disadvantage. Just when they thought all hope was lost, Ohtomo drills his way up from the ground in a vehicle being used as a Space Expo exhibit, but their relief is short-lived...
Hanasaki left Kobayashi behind and took off for Twenty Faces' hideout alone, planning to put an end to everything. But Kobayashi can't accept that, so he follows him... even though the aura surrounding him has already disappeared. Unaware of this, Hanasaki reaches the hideout and finds Akechi, but Twenty Faces also appears and warns him that the hideout will soon be destroyed. Hanasaki throws Akechi into an escape shuttle and turns toward Twenty Faces, with his finger on the trigger.
