Li Shanshun is a Chinese student just moving to Japan. Upon moving in his new apartment he meets a woman named Haraguchi. He sees here again that night, after observing the stars, and even saves her from getting caught by the cops. It seems Haraguchi is in something she shouldn't be as Li saves her from being kidnapped after running into her again. But a second rescue is out of the question since the kidnapper is a Contractor. Li is knocked off a bridge and left for dead and Haraguchi is taken away. Is Li really dead? Or is there more than meets the eye when it comes to him?

Not long after the appearance of the gate, a group went in to investigate the gate. Among the group only one man survived. Tahara now spends his time in his office taking care of the flower he found in the gate. But things are about to change as a group targets him for his research on contractors and the gate. Can Hei and the others get the information first?

Gai and Kiko get hired by a widow and are asked to find the widow's lost black cat. While trying to find the cat, they meet Hei, who is looking for the Contractor that is killing employers from that same company. As both Gai and Kiko continue to look, Gai comes across the skeleton of a woman who has been dead for a while.

As Gai investigates the murder of Toshiko he is attacked by the mind switching contractor, who wants his jacket back. Mao makes an attempt to steal the jacket and take off with it by switching bodies with a crow. He fails and must revert back to the cat body. Things don't look good for Mao when the contractor realizes who he is. Now Mao's life hangs in the balance, can hei get there in time to save him and kill the contractor?

Misaki finds herself reunited with her old high school classmate, Alice, who is also the daughter of the boss of the Hong Kong mafia, Chen Long Tang, on the night of Alice's birthday party. At the party, Misaki finds that her working collaborate, Saitou, along with Hei, have snuck into the party as well. Unfortunately, Misaki finds out that Alice and her Contractor Bodyguard Wei Zhi Jung have been responsible for the deaths of many of the mafia members.

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.

A group of Contractors, called MI-6, capture a once deadly Contractor called Havoc, who has lost her powers. Upon retreiving her they take her to Tokyo to be experimented on by the Pandora Institute. After watching a helicopter take Havoc away Misaki meets Jack Simon aka November 11. Later on as they are driving down the highway, Misaki finds out that Havoc really isn't on the helicopter. Where is the real Havoc and how does Hei know her?

As Li and Haraguchi continue to avoid Alan and the other Contractors, Haraguchi reveals that her actual name is Chiaki Shinoda. She also says she will give him the information she received from Rui. Upon retrieving the information Lee leaves Chiaki behind and takes of with the information. But everything is not as it seems. After getting a little ways away Li is attacked by Alan and the other Contractors. Can he survive?

Things have taken a turn for the worse, with Tahara's daughter being a contractor, but not being able to control her powers. Now Mai has been kidnapped and the group responsible wants Tahara's research or they keep Mai. Things may not go as they plan when Hei gets involved. Will he be able to get Mai back?

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.

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?

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?

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?

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.

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?

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.

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.

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.