Eric Nishijima is using a particle accelerator to wipe out the contractors. Amber gathers numerous contractors to destroy the accelerator, and dolls to be used for some other unknown reason. Nijishima is related to the Syndicate as he places a phone call to eliminate Hei and his team. Amber sends a message to Hei via Wei, telling him to meet her in the Gate. Hei agrees and thus Huang, Mao, and Yin, agree to assist Hei to infiltrate Hell's Gate with Wei's guidance.

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.

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.

A doctor is abducted by agents of the EPR, while the American embassy in Tokyo suffers attack from Hei and his team. A new contractor with the power to teleport herself and others appears as a double agent for the EPR. Wei Zhi Jung reappears, but is scarred from his last encounter with Hei. Misaki enters the embassy compound only to be detained by PANDORA, and Mao is discovered by Amber. November 11 leaves the M16 for the EPR.

Mao is taken by Amber to the headquarters of the EPR. While there, Amber calls a meeting for all of the EPR's contractors, including Mao, and the Doctor. She reveals that there was a plan to destroy the South American gate, which would have led to the eventual disappearance of all world-wide contractors. The Doctor notes that the plan was interrupted by a mysterious blue light. November 11 meets the head of East Asian MI6 operations, who is revealed to be a member of the Syndicate, and they kill each other. Hei attacks the EPR to rescue Mao. Hei uses his powers on Amber while Amber activates her meteor shard, resulting in the illumination of the whole building in a blue light.

After meeting with Amber, Hei learns that against common knowledge Contractors can become more humane than was thought to be possible. Realising his own position between the world of contractors and humans, Hei has to make the decisive choice for both. With final farewells to his past comrades inside the Gate, and their support behind his back, Hei's decision brings new future for the world.

Suo encounters someone she thought was dead and learns the truth behind the mysteries of her past. Unfortunately, the meeting is cut short when several Contractors launch an attack.

Kastenin, Gai, and Kiko take Yin back to her home town, meanwhile Hei is given the order to kill Yin and is given her location. Getting to Yin is not going to be that easy since th contractors from before are still after Yin and have their own method to finding her. The race is on once more, but this time Hei must make the choice on whether or not to kill Yin. Will he kill her or will the option be taken from him?

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.

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.

Hei learns the truth about the mysterious Izanami. If BK-201 wants to reach the object before it's destroyed, he'll have to defeat Genma - and stop Suo from pulling the trigger.

Suo and July find themselves in a dangerous situation thanks to a double-crossing supposed ally. Later, when the young pair is abducted by an especially sinister Contractor, BK-201 must spring into action.

Tokyo is locked down as chaos follows Amber and the members of Evening Primrose. The Black Reaper knows the destruction that can be unleashed if Amber isn't stopped - and he's willing to risk the wrath of his own team to thwart her.

Prophesies are fulfilled, and Suo faces her destiny. Even as her memories fade away beneath the shining moon, hope remains - and a new era begins.

An Eurasian girl named Suou watches a meteor shower along with her twin brother Shion and their father, but things go awry when a meteor crashes into their location. Two years later, Shion has turned into a contractor from the incident, confined to a wheelchair due to his renumeration. He is locked away into the family home for safekeeping, while Dr. Pavlichenko spends his time researching into his son's condition and the contractors, forbidding Suou to talk or see her brother. Things go normally in their lives until Suou's best friend Tania becomes a contractor and attacks her boyfriend Nika when he stops her from leaving. Hei aka BK-201 reappears in Russia after a FSB squad tries to capture Shion alive; April also reappears in Russia on a mission to secure Shion.

Hei and Suo attempt to flee Russia, but their escape efforts are hindered by Contractors and gun-toting soldiers. As the body count rises, Suo finds herself undergoing a shocking metamorphosis.

Aboard a speeding train, Hei's team is ambushed by Russian authorities. In the ensuing battle, Suo and Tanya recall the times they shared in the past as friends - and clash violently in the present as Contractors.

Havoc is iterrogated by Hei on the whereabouts of Amber and Pai (Who is Hei's younger sister) Unfortunately, Havoc does not know anything useful. She offers to help Hei by approaching the Gate and recovering her memories and powers, but that only leads her to wanting her own death. With the MI6 agents in pursuit, her wish may be granted.

Kenji falls for the doll, and they try to run away together with Hei's help. While out shopping, Hei is nearly identified by Kirihara Misaki as BK201, but Misaki doesn't see the relation between Li Shunsheng and BK201. Later, Kenji is caught and nearly killed by the boss, his brother, when Hei saves him. Kenji and the doll successfully run away.

Hei is sent to infiltrate a religious organization and kill the Prophet, Alma. He is aided by an insider, another Contractor by the name of Shihoko whom Huang appears to know. Amagiri and Alma appear to be in cahoots with Alma providing him with dolls. A well-meant mistake on Huang's part leads to Shihoko's capture.

In Japan, Suo begins honing her combat skills under the watchful eyes of Hei and July. Meanwhile, Kirihara - still puzzled BK-201's disappearance - gets acquainted with the agents of Section 3.

After Section 3 pushes Suo and Hei deeper underground, BK-201 must resurface to steal an object known as Izanami. The mission could get complicated - the agent tasked with guarding the object is none other than Kirihara.

Kiko and Kurasawa help Suo search for her mother. After a mysterious stranger points the young Contractor in the right direction, a long-awaited reunion leads to an unbelievable revelation.

After Hei and Misaki barely escape from Alice, Hei goes his separate way after Misaki and Saitou find each other. After Hei steals the crystal hidden within the stone flower garden, he runs into Wei and loses the crystal in the process. Wei finally meets up with Misaki and Saitou, who have found Alice. After Wei kills his partner, Alice, he moves in on Misaki and Hei.

Nick and a few other researchers are sent into the restricted section of the Gate to retrieve what is to believed to be the meteor fragment. Everything goes wrong and the entire team ends up dead, except Nick. Now Hei realizes that Nick is a contractor too, who seems to have the same power, and he also has the meteor fragment. Upon confronting Nick, the two begin to fight. Can Hei defeat Nick or will something else end the battle?