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?

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 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.

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.

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.

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.