A Special Religious Zone is established, where immigrants can practice religion freely. Religious leaders gather for a press event in Mitake New Town, the site of the Special Zone, but the venue becomes the target of a terrorist attack by a suicide bomber with explosives implanted in his stomach. Unit One starts investigating the anti-special-zone faction.

Unit One has begun to grasp the truth behind the incidents following each other like a line of falling dominoes and team up with the SAD to continue their investigation. Arata guards the governor, who is at risk of being targeted again, while Kei organizes a sting using Kisaragi as bait. When he arrives at the appointed meeting place, however, he finds Shizuka Homura waiting for him.

Tokyo, 2120. A massive transport drone crashes, and Unit One’s new inspectors Arata Shindo and Kei Mikhail Ignatov head to investigate. Discovering that Hyper Transport Co. accountant Asahi Rick Fellows is missing, Arata performs a Mental Trace to track him, but finds only his waterlogged corpse. Arata and Kei suspect the crash was staged, and pursue the mastermind who tried to silence Rick.

After meeting Karina Komiya face-to-face, Arata senses something unfathomable from her, but can’t find a clue to the case. Then Lee Aki, the secretary of her opponent, Kosuke "Heracles" Yakushiji, is murdered. Unit One decides to split up to investigate both the attackers and their victims, but…

Arata and the others have just learned that there are three more human bombs when a third suicide bombing in New Town’s factory district takes Joseph Auma’s life. Meanwhile, Kei and Kisaragi have infiltrated Heaven’s Leap in search of clues to the terrorist serial bombings. They discover proof they’re looking for, but find themselves exposed and taken captive.

While Kogami is recuperating from Akane’s Paralyzer shot, she begins to worry about whether she is suited to be an Inspector after the fallout from her first case. On her second day on the job, she begins to learn more about the Enforcers she works with.

Right before Kitazawa was executed, he mentioned the name of someone who had supposedly been helping him. While others just think that he was crazy, Akane wants to get to the bottom of this case and tries to seek out help from someone.

Freelance journalist Yayoi Kunizuka joins Unit One as an investigation consultant to fill the gap left by Kei’s suspension. As the investigation progresses, Unit One uncovers Karina Komiya’s greatest secret. Guessing that Karina will be the next to be attacked, they rush to her gubernatorial debate at the Giga Arena.

Through a Mental Trace, Arata discovers that the supposedly-dead Kurisu is alive and uncovers the truth behind the terrorist bombings. Shimotsuki, meanwhile, has launched a forced search of Heaven’s Leap and brought Unit Two to locate Kei. Torri, cornered, takes Maiko hostage and confronts Kei, but Maiko takes advantage of a momentary opening to end his life.

A series of bombings takes place in Tokyo. After some analysis, the detectives figure out who the culprit is and his whereabouts, and head to his location. Akane wants to be cautious, but the other Inspectors decide to rush in, and...

Taking place three years prior to the series, the episode focuses on Yayoi, who was a guitarist in a band before being imprisoned in a rehabilitation facility for being a latent criminal. As she anxiously waits for release so she can play the guitar again, she is approached by Kogami, who was still a detective, and Ginoza about a series of crimes occuring in the area she was once familiar with. She initially rejects their offer until Kogami gives her some guitar strings which reminded her of a guitarist she admired, Rina Takizaki. When the club they are investigating gets set on fire after Kogami's partner Mitsuru Sasayama jumps the gun in approaching culprits dealing with molotov cocktails, Yayoi decides to search for Rina, only to discover she is part of a resistance group selling the molotov cocktails in the hopes of overthrowing the Sybil system.

An Enforcer from Division 2 was executed by a Dominator and an Inspector from the same division has gone missing. The only clue they have is the mysterious message “WC?” left at the crime scene. But who could commit a crime without being detected?

Ginoza and Akane, along with the Enforcers, are brought in to investigate a death caused by a Drone at a Drone manufacturing plant. When the Psycho-Pass of the entire staff checks out, they question whether it was an accident or possibly murder.

When the CID is brought in to investigate a disappearance of Kimihiko Hayama, they discover that not only has he been killed, but someone has taken over his net avatar, Talisman. The CID tries to track down the fake Talisman in order to find the killer.

After reading Kogami’s personnel file, Akane attempts to learn more about Kogami’s past and why he ended up as an Enforcer. Meanwhile, the CID detectives attempt to figure out who was helping Kanehara commit murders in the Hachioji Drone incident.

After realizing that the recent murders and the Specimen Case are indeed connected, Ginoza takes Kogami off the case and requests Tsunemori to watch over him. Tsunemori discusses Sasayama's murder with Kogami, and he gives her his one piece of evidence: a blurry image of Makishima. Meanwhile, Makishima, in a study with another older man, reveals the circumstances of Rikako Oryo's father's death and discusses the nature of the shortening life expectancy in this "perfect" world. Later, Rikako continues her crimes with the help of Makishima's colleague, Choe Gu-Sung, and abducts another fellow student who is worried about her friend's disappearance.

The MSPWB has identified a possible hiding place for Kamui, and Divisions 1 and 3 are sent to the scene in order to investigate. Meanwhile, Akane has Saiga help with Representative Masuda’s interrogation.

Multiple Dominators were stolen by Kamui during the massacre caused by the Military Drones. Who does he intend to use those Dominators on? And why hasn’t the Sibyl System taken any action to deactivate them? Akane goes to see Kasei to get answers.

Kamui has been hiding in plain sight using Holos that take the form of dead people aged up, which makes Akane realize that his actions have been planned in great detail. Meanwhile, Mika closes in on the truth about Kamui and submits a report to Kasei.

Unit One chases a suspect in the staged crash, Hyper Transport Co. executive Takumi Yonehara, into an abandoned zone. But when they track Yonehara down, they find he’s already dead. Arata and Kei ignore Chief Shimotsuki’s orders and pursue the mastermind, Sasagawa, to Ariake Airport, where two unfamiliar men stand in their way: Shinya Kogami and Nobuchika Ginoza of the Ministry of Foreign Affairs.

The CID’s hunt for Kimihiko Hayama’s killer leads them to another murder with the same modus operandi. Now it’s up to the CID to figure out how to track down the killer’s real identity and get justice for the victims.

Kogami, attempting to track down Makishima, takes Tsunemori to visit his former teacher, Jouji Saiga, who agrees to give her a crash course on criminal profiling; however, Ginoza reprimands her harshly which results into an argument. Afterwards, Masaoka explains to her Ginoza's attitude by revealing his past. In the meantime, Makishima discusses humanity and philosophy with Senguji, who in an earlier interview reveals himself to be nearly a full cyborg. He gives him his next target: Shinya Kougami.

Ginoza meets up with the head of the Public Security Bureau about Makishima, who confidentially reveals to him about the real culprit of the Specimen Case, Touma Kouzoburou, three years ago who happens to be "criminally asymptomatic" just like Makishima. She urges him to keep any doubts away from the public eye and orders him to capture Makishima. Following Yuki's funeral, Akane agrees to undergo a 'Memory Scoop' to provide a photofit of Makishima based on her memories of the incident, despite warnings from others that it may damage her Psycho-Pass. Despite reliving the traumatizing memory, the Memory Scoop is successfully completed without her Psycho-Pass reaching into dangerous levels, providing a photofit image of Makishima to aid in the investigation. Later, Ginoza discusses with Masaoka, who is actually his father, about how Akane manages to keep her Psycho-Pass from becoming unclouded.

Ginoza, whose Hue is now problematic, eschews intensive therapy in order to work on retrieving Kogami and Makishima. He argues with Masaoka over his "softness," and declares his intention to see his "obsession" through to the end. Kogami, meanwhile, goes to visit Saiga in order to figure out Makishima's next move; the two surmise that Makishima might attempt to meddle with Japan's food supply in order to force open borders for the country. Shion does her best to comfort Akane and Kasei connects with Sibyl to determine their new "pawn." Later, a Dominator-bearing drone comes to visit Akane in the office - and declares that it will tell her the truth about everything.

The Military Drones hunt down the MWPSB detectives. While attempting to evacuate the detectives, Akane realizes what Kamui’s true objective is. Meanwhile, the Analysis Lab rushes to track down and deactivate the program that hacked the Drones.