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.
Before Hei could obtain the Meteor Core from Suou, Hazuki attacks him in order to secure Suou. Suou sought sanctuary alongside Nika to avoid being captured by FSB agents due to the events regarding Tanya's Contractor powers being known and for Suou being mistaken for Shion. When Hei tries to recapture Suou, he tries to obtain the Fragment when he realizes that "Shion" is actually Suou, which greatly changes Hei's mind of securing her when a FSB squad ambushes Hei. Hei escapes with Suou along when August 7 and Genma attack the FSB squad separately to secure Suou for their own objectives. Hei and Suou were caught in a trap after Hei seemingly kills August 7 by electrocuting the British contractor. Later on, Misaki is shown looking through a telescope which is directed towards BK201's star. The star fades away.
The trap devices holding Hei explodes from the energies caused by the meteor fragment. Suou goes into a daze and shove both herself and Hei into the sea. Hei awakens in a hut with Suou in tow. After a tense exchange, Hei decides to bring Suou and leave Vladivostok. Hei and Suou try to make their escape at the train station while Nika distracts Tania from her mission. Misaki is questioned by an MIAC official named Kobayashi about the contractors and the Syndicate. She is given an offer to join MIAC in pursuing BK201 who is revealed by Kobayashi to be alive. Hei, Mao, Suou and July, who has joined up with them, rides on a ship leaving Russia.
Hei and the others landed in Sapporo, taking refuge in an uninhabited part of the city as half of it was previously flooded. Misaki was recruited into the MIAC's black ops division Section 35 and was given the alias of Yayoi Ichinose. Hoping to learn what happened to Hei, she sought out an informant to obtain information of what happened to him. Hei decides to train Suou given that she has obtained Contractor powers after the previous gunfight against FSB forces in Vladivostok. Despite Suou's hatred to Hei for changing her life, she decides to stay with him alongside July. Meanwhile, Misaki heads to the now abandoned National Observatory when she was confronted alone by Madam Orielle, who knows of her real name aside from her alias.
Hei was attacked by a group of MIAC agents led by Michiru, the wife of a local restaurant owner who left him three years ago after being a Contractor for the MIAC. Suou and July were able to escape capture from the agents under Hei's instructions. Misaki is tasked by the MIAC to lead a Section 3 unit in delivering a device with the codename as Izanami under orders from Kobayashi. Hei recruits Suou to assist him in launching a raid on the Section 3 convoy under orders from his employers to seize Izanami with the mission seemingly a success after the truck drives away in the attack. Michiru appears to her family in Sapporo, startling her ex-husband and son. Suou watches the waters of Sapporo after the mission, seeing an unknown submarine covertly entering Japanese territorial waters.
Hei engages Genma in a battle, taking in the trap prepared by Misaki while she and the rest of Section 3 prepare to transport Izanami to the Greater Tokyo Area via submarine. Suō and July are tasked by Mao to take down the metal container that houses Izanami. Hei, after realizing that Yin was in the container all along, interrupts Suō's attempt to shoot it and instead retreats. Hei and the others retreat from Sapporo also, heading to Tokyo after Suō witnesses the death of Michiru when a specter resembling Yin strangles her with her water powers. Misaki is later warned not to think of Yōko as an ally. Hei then goes rogue once more, cutting off connections with Madam Orielle. When Suō sees Yin's specter from the electric pole, she kicks it before walking with Hei back to their hideout.
Misaki and Genma meet at the abandoned National Observatory, the former being warned that communications between her and the rest of the world are being tapped by the MIAC. Hei and the others escape from Sapporo under a heavy police lockdown by seeking assistance from the underworld. However, Hei is later duped when their contact gets away with kidnapping July. A Russian agent named Ilya Sokolov encounters Suō and uses his Contractor powers to help him detain her, Mao and July after killing their contact. Hei later comes to their rescue and kills Ilya, despite nearly being overpowered by Ilya's powers. The four later were able to arrive at the Sendai Shinkansen station, boarding it while Repnin of the FSB watches them from his cabin.
Suō recalls a summer day in Vladivostok before the series when she played with Tanya by a pool. Meanwhile, Hei is intercepted by Repnin's men in the train hallway and Suō is confronted by Tanya. Repnin offers Hei a job with the FSB after inviting him to eat. During this time, Hei and Misaki are told simultaneously that Izanami has the ability to cause contractors to commit suicide. Hei refuses Repnin's offer and attacks him, while Tanya summons a swarm of insects to stop the train and escape with Suō. Outside the train, Hei and Suō face off against the FSB force on their own, defeating them. Unknown to Suō, Tanya was killed by Suō's brother Shion from a nearby rooftop. As Tanya floats in the stagnant pool, Suō ponders that she can never return to the innocent summer days she remembers. Suō later heads off to Tokyo with Mao and July on their own without Hei to guide them.
As Suō and July ride a train through Tokyo Suō collapses from a high fever, waking up in Kiko's bedroom. Kiko and Gai decide to help Suō search Tokyo for Suō's mother, but with little success. Misaki finds a recording by Amber which instructs her to find a certain CD, which informs her that Izanami will eventually meet Izanagi, at which point Hell's Gate will open. Following the advice of Madame Orielle, Suō proceeds to an airport to find her mother. At the airport Hei appears and kidnaps one of Misaki's teammates, easily evading Mina and escaping. Suō's mother cries upon meeting Suō in the airport, believing she is her twin brother Shion. In a car Suō tries to explain that she is not Shion, but her mother dismisses this saying that Suō died 8 years ago.
Suō tries to remind her mother of the happy time they visited the aquarium, but flees when she denies it. Misaki finds Suō in the cold and explains that the aquarium she remembers was demolished 13 years ago. Suō's mother recounts to Misaki that day 8 years ago in Moscow when she took Suō and Shion to see her husband Dr. Pavlichenko at the university; Mao was also present then and lost his body in the explosion. Suō's mother remembers seeing her husband manipulating Suō in a machine, then fleeing with Suō's lifeless body while Shion watched from a window. Shion reveals his ability: He can create a perfect clone of any organism. Hei rejoins Suō, July, and Mao after incapacitating Misaki. Mina vows to kill Hei upon finding Yoko's bloody corpse.
Hei decides to leave for awhile to settle his own problems. After which, Suō decides to do the same - going to find her father and ask him about her. Suō, July and Mao go to the aquarium and they find Dr. Pavlichenko there. He tells Suō the truth about the meteor incident that year and about Shion's abilities to copy. On the other hand, MIAC head for the aquarium and Genma bumps into Suō and gang. Misaki bumps into Madam Orelle and she tells her to follow because there will be a bloodbath soon. Suō and gang run and hide, but Dr. Pavlichenko is shot by a contractor while trying to protect Suō. They hide somewhere while Genma calls for Suō. Suō tells the rest to hide while she confronts Genma herself. She manages to knock out Genma in the battle, but gets back to the rest only to find her father dying. They leave while MIAC finds Dr. Pavlichenko's body, with Suō's origami of a star on him. Meanwhile, Hei tries to find Yin, but was surprised to see the containment empty. Mina comes out and attacks Hei. Back at the Gate, Misaki meets with Mao and July, only to have found Suō disappeared. It is shown that she found Shion on the floor, unconscious.
When Suou finds Shion collapsed, Shion explains that it’s because he paid a suitable remuneration. He then asks her to take him outside because he wants to see the moon, and by the time Misaki and company arrive, the two are gone. Hei meanwhile finds himself locked in battle with Hazuki Mina, and she’s eventually able to tie him up. After kissing him as part of her remuneration, she prepares to kill him, but Kobayashi steps in and reveals that it wasn’t Hei who killed Youko. The real culprit was Shizume Genma who had betrayed them for the CIA, and the Americans have taken over control of most of the organizations inside and outside Japan. Given all this, Mina has Kobayashi and Hei go on ahead while she goes to take care of Genma, and Kobayashi takes Hei to where Yin’s body is. The body, however, is now only an empty shell, and Yin’s awakened spirit has gone to the center of the Gate. By now, Madame Oreille has brought Misaki and Mao to a building that houses a super-computer created by Dr. Pavlichenko. In it are rows of bodies that look like Shion, and Madame Oreille explains that the super-computer has all records of the world as observed by the Doll Network and all memories of mankind gathered by the ME Network. It was all for Shion’s plan, and Madame Oreille reveals that the moon isn’t really a moon - it’s another Earth created by Shion’s ability. At this moment, unaware of all this, Suou is pushing Shion in his wheelchair somewhere inside the Gate. In talking about Suou’s memories, Shion reveals that he only imagined human-like memories and put them in her and that his dream isn’t a reflection of those memories. He also notes Suou’s sentimentality despite being a Contractor, and Suou attributes it to the influence of the people she traveled with. The two then come across the dead body of a Contractor, and Shion disappears in that instant. Suou searches inside the Gate for Shion until she comes across one of July’s observer spirits. While she’s following it to him, July is being found by August 7 who tells him that their operation is over. July, however, refuses to go with August 7 and chooses instead to stay with Suou, so August 7 lets him go and disappears. Suou arrives just moments later, and after hugging her, July leads her to Shion and Yin. Suou finds Shion almost dead, and in his final words, he tells her that the deal is done and that he wants her to see the world he created. His spirit then goes to Yin, who is floating above them, and Yin tells Suou that she granted Shion’s wish. At this point, July collapses as well, and, still not really understanding what’s going on, Suou decides to bring out her gun against Yin. This leads to Yin breaking the meteor core on the necklace that Shion is wearing. As Madame Oreille explains to Misaki and Mao, when they copy a person and implant memories, they can’t establish it for long without the meteor core. They thus used Suou and her journey here as an experiment to make sure that Suou’s memories had set. What this means for Suou now that the meteor core is destroyed is that her memories are leaving her. Realizing what’s happening, Suou tries to resist the loss of memories and aims her gun at Yin again in a last ditch effort, however Hei shows up and stops her from shooting. As he holds her, he tells her that she won’t be needing her gun where she’s going next, and he promises that he’ll always be with her. He lays her down beside July after she loses consciousness, and Yin then tells Hei that it’s not too late to kill her. By the time Misaki arrives on the scene, she sees BK-201’s star lighting up in the sky, and a bright light envelops Yin as she’s touched by Hei. In the aftermath, Suou lives a normal life with both her parents on the copied Earth. She can sense that something is lacking, and though she’s not lonely, she feels that she knows a certain someone very well and believes that she’ll meet this person someday. Back on the real Earth, Kobayashi thinks that it’s all over, but Misaki feels that things are just beginning, and Madame Oreille picks them both up. They then leave the Gate and start operating independently since America and other countries now control Tokyo, and ironically, they become known as the Syndicate. What they don’t know is what the prophesied newly born thing is and how it will change the world. Unbeknownst to them, a boy resembling Yin wakes up inside the Gate and absorbs the spirits of John Smith and his men. Regardless, Misaki notes that she hasn't heard of Hei again, but she continues to believe that he’s still alive.