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.

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 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.

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.

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.

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.

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.

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.

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.