Thousands of years ago, the ancient dragon Bahamut wrought havoc upon the land of Mistarcia, a world where both gods and demons live amongst mankind. Working together to prevent the world's destruction, the rival deities barely managed to seal Bahamut, agreeing to split the key between them so that the dragon would remain eternally imprisoned. With the world safe from the destruction of Bahamut, it is business as usual for bounty hunters like Favaro Leone. Living a laid-back, self-serving lifestyle, the amoral Favaro goes about his work while on the run from fellow bounty hunter Kaisar Lidfard, a righteous man who swears vengeance upon Favaro. However, Favaro's carefree life is thrown into chaos when he meets Amira, a mysterious woman who holds half of the key to the world's fragile peace. Shingeki no Bahamut: Genesis tells the story of a group of unlikely heroes who find themselves caught in the middle of an epic clash between gods and demons, forced to carve their own path in the face of the imminent storm.

The story begins on a rainy night, when a homeless little black cat is brought home by a young girl Luo Xiaobai. She names the cat Luo Xiao Hei. However, Luo Xiao Hei is no ordinary cat: he is a supernatural entity that hosts several small creatures called Heixiu. As Luo Xiao Hei new life soon threatened by the mysterious Diting, who commands three winged wolves.

Nearly twenty years into the 21st century, people have forgotten the existence of youkai. When a number of unexplainable phenomena plague adults of the human world with confusion and chaos, thirteen-year-old Mana writes a letter to the Youkai Post in search of answers, only to be greeted by Gegege no Kitarou...

At the millennial edge, the concluding battle for humanity's future is staged. Kamui Shirou's destiny has been decided as he returns to Tokyo to face his ultimate challenge. The Dragon of Heaven, defenders of the Earth, stand ready to protect the world from the Dragon of Earth, the seven angels of legend, who embrace the devastation of the planet to bring about its purification. Now Kamui must decide which side to fight for although he finds the idea utterly unappealing. It isn't until realizing that his two childhood friends, Fuma and Kotori Monou, are in grievous peril that Kamui decides to step into his fated position in the climactic struggle of the Year of Destiny: 1999.