Kogami assists the rebel forces with a sniper rifle.
Tsunemori joins Colonel Nicholas Wong in an anti-rebel operation outside the city which sends an army of drones and mechs to fight the guerrilla. Tsunemori eventually spots Kogami fighting alongside the militia and abruptly exits Wong's armored tank in pursuit of Kogami. When they finally meet, Tsunemori and Kogami engage in a short brawl. Tsunemori consequently puts Kogami under arrest, however, they are suddenly attacked by one of Wong's tanks, forcing the duo to flee to safety. Tsunemori decides to follow Kogami to the rebel base to learn more about his involvement with the guerilla.
The Colonel is irritated by Tsunemori's actions, hiring bounty hunters to kill both her and Kogami. As Tsunemori observes life at the rebel base, she notices Kogami's influence within the community and warns him of becoming a second Shogo Makishima, a figure that influences those around them to resent the present social system, then assures him that he is ultimately different from Makishima due to their differing motives. Kogami suggests Tsunemori stay the night, promising to return her to the city the following day. The bounty hunters, led by Desmond Rutaganda, arrive during the night in search of their targets and begin attacking the guerrilla base. One of Rutaganda's thugs, Yulya Hanchikova, silently infiltrates the rebel base and kills the watchmen while Bun flies over the base using a jetpack to locate Kogami and Tsunemori while the rest of the team hold off the guerrilla with their bio-suits. Kogami tells Tsunemori to escape while he stays behind with guerrilla leader Sem in order to fend off the attack. As Tsunemori flees in a guerrilla convoy, Kogami and Sem rush to the warzone. Sem is abruptly killed in an explosion while Kogami is captured alive and tortured by Rutaganda, Jean Phillip Weber, Yulya Hanchikova, Bun, and Babangida.
Nhan Yeo is shot by Colonel Wong.
Tsunemori returns to the city and is arrested by Wong for defying his orders. She's to be sent back to Japan the following day, however, SEAUn Chairman Chuan Han arrives and tells Wong to let Tsunemori stay, under the close supervision of the military. Tsunemori returns to her room and eventually connects with Shion Karanomori in Japan, asking her to verify the legitimacy of the Sibyl System used in Shambala Float. As they speak, a servant named Nhan Yeo enters with Tsunemori's meal, including a glass of water laced with a sedative. Tsunemori drinks it and passes out, awakening to see Yeo asking Colonel Wong whether her brother could be freed after complying with Wong's order to drug Tsunemori. In response, she is shot at point blank range. Tsunemori fully awakens, but is placed in Wong's custody.
Kogami frees Tsunemori using Wong's gun and asks her to find the Chairman.
Back in Japan, Karanomori realizes that the Sibyl System in Shambala Float has been illegally modified to cover up the true Crime Coefficients of members of the military, which is comprised of latent criminals with Crime Coefficients well over 300, including Nicholas Wong. Wong devises a cover story stating Kogami took Tsunemori hostage in a helicopter which they had no choice but to shoot down, effectively killing them both. Tsunemori and Kogami are brought to the rooftop for execution by Bun but before the plan is carried out, the combat drones suddenly go under Sibyl's control, enforcing order in Shambala Float. Bun is shot dead by a Sibyl-controlled bot, prompting Weber, Hanchikova, and Babangida to flee. As Wong prepares to take matters into his own hands by drawing his pistol, he is eliminated by Nobuchika Ginoza wielding an Assault Dominator. Wong's army retaliates by shooting at the renegade drones, only to be decimated by the drones' deadly gatling guns. An aircraft fires missiles which results in the death of Hanchikova, who accepts her fate. Kogami frees himself and Tsunemori by using Wong's gun. Rutaganda takes this opportunity to escape, with Kogami in pursuit. Tsunemori is reunited with Division 1 which leads an operation to take down the rest of the mercenaries while Tsunemori seeks to arrest Chairman Han.
Division 1 learn of Han's resignation (from left to right : Mika Shimotsuki, Teppei Sugo, Sho Hinakawa, Yayoi Kunizuka).
Meanwhile, Kogami pursues Rutaganda, but begins having an hallucination of Makishima who questions Kogami's sense of justice while noting the risk Kogami is taking by pursuing Rutaganda. Kogami fires upon the apparition in anger and continues toward his target. Finally meeting his enemy, the two fight in an industrial complex. Kogami severs Rutaganda's cybernetic arm, but is pinned down at knife point. Ginoza suddenly appears, kicking Rutaganda off. During the brief fight Ginoza has with Rutaganda, his Dominator is destroyed but Rutaganda is pinned down once more. In an attempt to eliminate both Kogami and Ginoza, Rutaganda tries to activate an explosive using a mouth detonator. Kogami realizes what is about to happen and snaps Rutaganda's neck. The bomb still triggers, prompting Kogami and Ginoza to jump off the body. Ginoza then holds a revolver to Kogami's head, but decides to hand the pistol over to him instead, commanding Kogami to never show his face around Division 1 again and delivering a swift punch to his former friend before he leaves the scene.
Tsunemori is seen arriving at Chuan Han's chambers where she scans him with a Dominator. It reads a Crime Coefficient of zero and it's revealed that Han is actually a body double provided by the Japanese government, the real Chuan Han having been taken out within two days of meeting Colonel Wong. She convinces the Sibyl-controlled Han to resign from office, which he does, broadcasting it to the entire Shambalan populace. In the end, Tsunemori and the rest of Division 1 return to Japan and Kogami continues to reside at the guerrilla base.