The first short story focuses on Favaro and Kaiser between the events of the first and second series as they visit Favaro's home village. The second short story shows Kaiser as a knight commander sparring with Jeanne, and sharing the reasons they remained as Orleans Knights in the aftermath of the final battle against Bahamut.

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.

After a daring escape from the Memory Museum, Sayaka Miki returns to Mitakihara City with unsettling news. Troubled by what she has learned, Sayaka reveals to Madoka Kaname and Homura Akemi the whereabouts of Mami Tomoe—but more importantly—the disturbing truth behind the existence of magical girls. Despite knowing the cruel fate that awaits them, the three quickly resolve to work together and save Mami once and for all. Meanwhile in Kamihama City, Yachiyo Nanami hunts various "rumors" in search of Hotel Fendt Hope, the headquarters for the Wings of Magius. The magical girl organization is Yachiyo's only lead in finding Iroha Tamaki, whose disappearance remains shrouded in uncertainty. Determined to reunite Team Mikazuki Villa, Yachiyo swears to destroy the Wings of Magius and put a stop to their insidious plans. Amidst the turbulent situations, a calamitous threat approaches, presenting a dire conflict set to jeopardize the entire world.

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.