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.

High school girl duo Popuko and Pipimi are back and more unhinged than ever after their initial efforts to create a full-fledged anime production were met with a great reception. With no regard for their audience, they continue to live their reckless everyday lives consisting of comedy skits and parodies of epic proportions. No one is immune to the effects of their antics—including hapless live actor Shouta Aoi, who is on the run and stuck trying to be a hero in the wrong series.

Thanks to Professor Yuuko Kouzuki's technology and Kasumi Yashiro's psychic powers, Cadet Takeru Shirogane travels back to his original world. With no time to lose, Takeru aims to enlist Yuuko's help in his world to complete the Alternative IV project—the last hope humanity has against the BETA, an alien species invading the planet. As the anti-BETA project nears completion, Takeru and other cadets graduate from the Yokohama pilot training academy. However, during a test of the new operating system for the Tactical Surface Fighters—the giant combat suits used by humanity against their adversary—the BETA ambush Takeru and his team. Barely escaping with his life, Takeru is left traumatized after witnessing the cruel death of one of his close friends. Losing his will to fight, Takeru flees back to the other world, where he experiences a similar tragedy. According to Yuuko's theory, people from parallel universes are bound to suffer the same fate. As a result, Takeru must overcome his trauma if he wants to protect the ones he holds dear.

Gaowei crossed in an airplane accident and appeared on the Loren continent as the ancestor of the Cecil family. In the face of the declining family, he re-expanded the territory, and in the face of class barriers, he used the wisdom of the people. But the crazy and stubborn cultists and the potential crisis of the magic tide are still there, how should Gaowei face the world that is about to usher in the end of the era...