The Organization orders Huang to kill Shihoko, and as a secondary directive secretly orders Mao and Hei to kill them and Alma if Huang fails. In Huang's past we see him falling for Shihoko, and then Shihoko killing his then police partner Isozaki. Isozaki's wife's memory is wiped by the ME, and Huang is drafted into the Syndicate. He is unable to kill Shihoko, and asks Hei to kill them both. Hei tries to help them run away while Mao refuses to have any involvement. When they arrive at the docks to wait for a boat, Shihoko sees someone from the Syndicate and realizes they cannot escape. For love of Huang she runs into the path of an oncoming truck and dies.

Hei's team, on the orders of Eric Nishijima, has been kicked out of the syndicate and contracts taken on all their lives. Misaki discovers that the "syndicate" is really a collaboration between intelligence agencies of multiple countries and that she herself has been an unknowing member. Hei, Yin, and Mao infilitrate Hell's Gate while Huang detonates a suicide bomb for distraction. Mao is disconnected from the Syndicate's network and his feral cat behavior takes over and runs away. The EPR's contractors attack the gate, leaving the focus open for Hei and Yin. The syndicate takes out the EPR's doll system, leaving Hei with only Yin for guidance as they head towards the conclusion of the story.