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.

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.

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...

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.

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.

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.

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.

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.