Li Shanshun er en kinesisk studerende bare at flytte til Japan. Ved at bevæge sig i sin nye lejlighed møder han en kvinde ved navn Haraguchi. Han ser her igen om natten, efter at observere stjerner, og selv sparer hende fra at blive fanget af politiet. Det synes Haraguchi er i noget, hun skal ikke være så Li redder hende fra at blive kidnappet efter at have kørt ind i hende igen. Men en anden redning er ude af spørgsmål, da kidnapper er en entreprenør. Li er slået en bro og efterladt som død og Haraguchi er taget væk. Er Li virkelig død? Eller er der mere end opfylder øjet, når det kommer til ham?

Da Li og Haraguchi fortsat undgå Alan og de ​​øvrige kontrahenter, Haraguchi afslører, at hendes faktiske navn er Chiaki Shinoda. Hun siger også at hun vil give ham de oplysninger, hun har modtaget fra Rui. Ved at hente oplysninger Lee forlader Chiaki bagved og tager af med oplysningerne. Men alt er ikke som det ser ud. Efter at have fået lidt måder væk Li angribes af Alan og de ​​øvrige kontrahenter. Kan han overleve?

Ikke længe efter fremkomsten af porten, en gruppe gik ind for at undersøge porten. Blandt gruppen kun én mand overlevede. Tahara nu bruger sin tid på sit kontor tager sig af blomsten han fandt i porten. Men tingene er ved at ændre sig som en gruppe rettet mod ham for hans forskning om entreprenører og porten. Kan Hei og de andre få de oplysninger først?

En gruppe af entreprenører, kaldet MI-6, fange en gang dødbringende Contractor kaldet Havoc, der har mistet sine kræfter. Efter retreiving hende de tager hende til Tokyo for at blive eksperimenteret på af Pandora Institute. Efter at have set en helikopter tage Havoc væk Misaki møder Jack Simon alias 11. november Senere da de kører ned på motorvejen, Misaki finder ud af at Havoc virkelig ikke på helikopteren. Hvor er den virkelige Kaos og hvordan Hei kender hende?

Havoc er iterrogated af Hei på opholdssted for Amber og Pai (Hvem er Hei lillesøster) Desværre Havoc ved ikke noget nyttigt. Hun tilbyder at hjælpe Hei ved at nærme Gate og inddrive hendes erindringer og beføjelser, men at det kun fører hende til at ønske sin egen død. Med MI6 agenter i forfølgelsen, kan der ydes hendes ønske.

Gai og Kiko bliver hyret af en enke og bliver bedt om at finde enkens tabte sort kat. Under forsøget på at finde katten, de mødes Hei, der er på udkig efter entreprenøren, der dræber arbejdsgiverne fra samme selskab. Som både Gai og Kiko fortsætter med at lede, Gai kommer på tværs skelettet af en kvinde, der har været død i et stykke tid.

Som Gai undersøger mordet på Toshiko han bliver angrebet af sindet skifte entreprenør, der ønsker sin jakke tilbage. Mao gør et forsøg på at stjæle jakken og tage ud med det ved at skifte organer med en krage. Han svigter og skal vende tilbage til den kat krop. Ting ser ikke godt for Mao når entreprenøren indser hvem han er. Nu Maos liv hænger i balance, kan hei få der i tiden for at redde ham og dræbe entreprenøren?

Misaki finder sig selv genforenet med sin gamle high school klassekammerat, Alice, som også er datter af chefen for Hongkong mafia, Chen Long Tang, om natten af ​​Alices fødselsdagsfest. Til festen, Misaki konstaterer, at hendes arbejdstid samarbejder, Saitou, sammen med Hei, har sneget ind i partiet så godt. Desværre Misaki finder ud af, at Alice og hendes Contractor Bodyguard Wei Zhi Jung har været ansvarlige for drabene på mange af mafia-medlemmer.

Efter Hei og Misaki flygte næppe fra Alice, Hei går sin egen vej efter Misaki og Saitou finde hinanden. Efter Hei stjæler krystal skjult i stenen blomsterhave, han løber ind i Wei og mister krystal i processen. Wei endelig møder op med Misaki og Saitou, der har fundet Alice. Efter Wei dræber sin partner, Alice, han flytter ind på Misaki og Hei.

Når en eksplosion er sat op til at stjæle en meteor fragment fra PANDORA hovedkvarter, er Hei sendte den til at stjæle det før nogen andre gør. På sin første dag møder han op Corinna Moku, der nedbryder ikke længe efter ankommer ved gaten, og Meena Kandaswamy, som er fra den samme organisation som Hei og vil hjælpe ham med at finde fragmentet. Nu Hei skal holde fra at blive opdaget som en entreprenør og finde meteor fragment. Men vil en død på hovedkvarteret bryde sit dække?

Nick og et par andre forskere bliver sendt ind i den begrænsede del af Gate for at hente, hvad der menes at være den meteor fragment. Alt går galt, og hele holdet ender døde, undtagen Nick. Nu Hei indser, at Nick er en entreprenør også, der synes at have den samme magt, og han har også meteor fragment. Ved at konfrontere Nick, to begynde at kæmpe. Kan Hei besejre Nick, eller vil noget andet afslutte kampen?

Hei, Yin, and Mao are targeted by a group of contractors and now must fight to survive. Things become problematic when Yin goes missing. Now Hei and Moa must find her before the enemy does, but things change when Yin's old piano teacher gets Gai and Kiko to find Yin for him. The race is on to find Yin, but who will get to her first?

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?

A sunspot called the Great Dark Spot, that makes the sun look like an eye, is about to appear and the last time it appeared the gate in South America dissappeared. To make everything even more hectic a boy is going around setting off explosions in the city. But things continue to fall apart when November 11 returns and it becomes apparent that Hei and November 11 are looking for the the same girl, who is known as Amber to Hei and February to November 11. Will Hei be able to find her before November 11 does, or will November 11 be taken out before his search can begin?

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.

Hei meets Sakurai Kenji of the Nakazawa Group, a clumsy yet ambitious young man. New characters are introduced who live in Hei's apartment building. Later, Kenji is given the assignment of taking care of a doll by his boss. Hei, Mao, Yin, and Huang try to find the doll, who is conveniently in the hands of Kenji.

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.

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.

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.

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.