Half a year after the battle in Okinawa, Excel was looking for a new Mototsumitama to revenge on Reishin. Excel met Mikami and decided to contract with her. Before making the contract, Excel looked back at the encounter with Steiner.

High school student Ibuki Keita has been haunted by misfortune for as long as he can remember. For no apparent reason, everyone around him dies tragically. Ultimately, he refuses to become too close to anyone, even his childhood friend Akane. This leaves Keita alone in a life full of misery and disgrace. While eating at his favorite ramen shop one evening, Keita meets a strange young girl named Kuro. Possessing abilities that surpass that of a normal human being, Kuro classifies herself as a Mototsumitama. She explains to Keita about Terra, a life-energy force split between three identical looking people; a global phenomenon dubbed the Doppeliner System. As a Mototsumitama, Kuro guards the Coexistence Equilibrium, the beings that protect the flow of Terra around the world. Keita refuses to believe her story, until he is caught up in the crossfire of this hidden world. On the verge of death, he makes a contract with Kuro, unbeknownst to its true meaning. Now he is bound to Kuro, and must be with her at all times. Could Keita's misfortune possibly get any greater?

In 12th-century Japan, swordsman Kurou escapes ghastly pursuers into a deep forest with his servant Benkei. Seeking shelter, the two find themselves within the secluded abode of the mysterious and beautiful Kuromitsu. While they are warmly accepted, the men are warned to never enter Kuromitsu's room. However, driven by innate curiosity and perhaps a condemned love, Kurou peeks through the ajar door, only to find Kuromitsu feasting on the blood of fallen men. He soon learns Kuromitsu is an immortal vampire, and dedicates himself to her—even becoming a vampire himself in order to spend eternity with her. But the cryptic organization known as the Red Army has enlisted the help of Benkei, who betrays Kurou and severs his head. Awaking centuries into the future in an apocalyptic modern-day Japan, Kurou sets off to reunite with his lover and exact revenge on the Red Army.

It has been half a century since humans took to the sky to hunt dragons. Although dragons present a great danger, every part of them is extremely valuable, and brave dragon hunters, called drakers, risk their lives aboard special dragon-hunting airships to pursue them. However, despite the thrill and excitement of hunting, the life of a draker is not easy. Ostracized by society, the drakers have no place to call home. Life in the air is not any easier either: maintaining an airship is dull and expensive—and dragons are even harder to catch, as each one is unique. One of the last remaining such airships is the Quin Zaza. Its courageous crew includes Takita, an eager newcomer trying to earn her place on the ship; Mika, a reckless but highly skilled hunter; and Jirou, an earnest young man chasing both the dragons and his past. United by the same goal, these hunters face arduous aerial battles that involve daring feats of skill, strategy, and more than their fair share of danger.