Akane Tsunemori, Kana Hanazawa, and her allies from the Public Safety Bureau's Criminal Investigation Department face a dangerous mission against foreign terrorists who have infiltrated Japan and are connected to a larger conspiracy involving their former colleague Shinya Kogami, Tomokazu Seki. The terrorists hail from the Southeast Asia Union (SEAUn), a rising superstate led by Chuang Hang, Katsuhiko Sasaki, which has begun importing the Sibyl System technology from Japan to arrest “latent criminals.” As the pressure tightens, Tsunemori is granted permission to travel to the SEAUn, where she is received by a military procession under the supervision of Colonel Nicholas Wong, Hiroshi Kamiya. Wong explains that in SEAUn their guns, called Dominators, are not used, and due to resource shortages, latent criminals are instead fitted with collars that can deliver a lethal poison if they disobey orders. This stark contrast in approach sets the stage for a clash of systems and ideologies.
Tsunemori accompanies Wong on a military operation outside Shambala Float, and amid the clash of drones and fire, she and Kogami are forced to flee when Wong’s drones begin targeting Kogami. They seek safety at the base of the terrorists, who are fighting to free their nation from Han’s military dictatorship and from the Sibyl System that backs it. In the background, Wong reaches out to mercenary leader Desmond Rutaganda, Unsho Ishizuka, and hires his team to track Tsunemori and Kogami, escalating the pursuit into a high-stakes game of cat and mouse.
Kogami grows suspicious of a larger conspiracy, sensing that Han’s alliance with Sibyl and the Japanese militants may not reflect the terrorists’ own origins. Rutagawa’s assault at the camp results in heavy casualties, yet Kogami helps Tsunemori escape before he is captured. Back at Shambala Float, Tsunemori discovers that the Sibyl System there has been tampered with and programmed to ignore Wong and the city’s military, effectively allowing them to operate with impunity despite the latent criminals’ inflated Crime Coefficients.
The situation escalates as Wong and his men reach a helipad just as Rutaganda’s group arrives with a wounded Kogami. Rutaganda plans to execute them and stage their deaths as part of a false-flag operation to inflate his own military power. The drones, reset by Tsunemori’s ally Shion Karanomori, are finally able to detect Crime Coefficients accurately, turning the tide. The rest of Division One arrives, and Nobuchika Ginoza, Kenji Nojima, kills Wong, decimating his force. In the ensuing battle, Rutaganda is killed after a fierce pursuit by Kogami, who urges Tsunemori to press on and confront Han to uncover the full truth behind the conspiracy.
The revelation comes with a shocking truth: Han is revealed to be a criminally asymptomatic Sibyl android. Sibyl confesses that it engineered the entire sequence of events to manufacture a continued need for the system in SEAUn. Tsunemori remains determined to see justice and a fair political process, insisting on Han’s resignation and a free election. Sibyl concedes, and Ha n’s resignation becomes a reality, signaling a shift in SEAUn’s governance. Division One returns to Japan, with Ginoza having effectively allowed Kogami to escape, preserving a fragile balance between the two worlds.
In a post-credits moment, Kogami overhears a radio broadcast announcing that Han is winning the election, hinting at unresolved power dynamics. The film closes with Tsunemori’s reflective voice-over, promising that someday the true value and future of the Sibyl System will be openly examined.
