When an explosion is set up to steal a meteor fragment from PANDORA headquarters, Hei is sent it to steal it before anyone else does. On his first day he meets up Corinna Moku, who breaks down not long after arriving at the gate, and Meena Kandaswamy, who is from the same organization as Hei and will be helping him find the fragment. Now Hei must keep from being detected as a Contractor and find the meteor fragment. But will a death at the headquarters break his cover?

The Stargazer of the Astronomical Bureau finally speaks, giving vague information on the Evening Primrose. November 11 kills Maki in a final showdown as Hei finally reaches Amber, who has taken Yin. Misaki also arrives at their location, but, with the help of Amber's contract, everyone escapes.

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.

Kirihara has searched long and hard for BK201?s true identity, and what she discovers of his past is shocking, but the impending destruction of Tokyo is foremost on the minds facing off in this final battle.

Sometime after the Tokyo Explosion incident, Hei had fought and defeated some Syndicate Contractors and had then fled with Yin to Okinawa. The two posed as newlyweds on their honeymoon, and Hei had tried to find a way out of the country. What began to bother him though was how Yin started acting on her own. The two ended up not leaving by boat because of the ferry ticket lady’s warning about Yin getting seasick, and this led to Hei running into a woman at the hotel who looked exactly like Amber. Yin noticed this as well, and after seeing Hei talking with the woman and later feeling distant from him, Yin had made use of her observation spirit that night. Although Hei had woken up and stopped her from doing anything drastic, Yin saw enough to be able to say that the woman was not Amber but was indeed a Contractor. Yin had tried to suggest that he get out of there, however Hei had just hugged her and vowed not to leave her by herself...

After having a dream where she’s being pulled on by a glowing child-like figure, Yin wakes up to Hei watching over her, and he promises to protect her. The two soon arrive in Hong Kong, and Hei finds a man named Chen to make some fake passports for them so that they can keep running. Yin, however, speaks out because she feels that it’s pointless and suggests attacking their enemies instead. She proposes spreading the rumor that he wants to sell her in order to lure their enemies in, and she believes that they can’t run away while there’s a Doll watching her. All of this plus Yin’s attitude worries Hei, but he decides to have Chen set everything up. While Chen is away, Hei questions why Yin didn’t tell him about the enemy Doll, but she seems not to remember what she said before. She does tell him though that she wants to be with him like this forever. Chen then comes running back because he encountered a dangerous group while spreading the rumors, but Hei is undeterred...