After the events of Ultraman Saga, Ultraman Zero goes to the Monster Graveyard to train with his new powers. There, Zero encounters Alien Bat Glacier; a follower of the original Bat that took over the alternate world. He revives the monster army, the Four Beast Warriors of Hell from the Graveyard to fight Zero for defeating his leader.

Zero finds himself trapped within a universal gap and faced against an impostor Ace. Following the battle, Darklops Zero was restrained once more by Herodia, remembering a figure named "Kaiser Belial" before deactivating. Rei was restrained after his failed attempt to intrude the alien base but was rescued by none other than his alternate self. Unlike the prime Rei, alternate Reimon was never able to control his powers, forced into the state of Reionic Burst until the original Rei punched Reimon, thus deactivating its Reionic Burst mode. Rei revealed that he lost his Rayblood instinct after Hyuga threw Seven's Eye Slugger, creating a scar on his chest which symbolizes the former's friendship with ZAP SPACY members. While searching for Rei, Hyuga instead finds his Neo Battle Nizer and an entrance to the alien base made by Litra. Although the fake Ace was destroyed, Zero try to find an escaped but was halted by Seven and Ultraman impostors.

Zero sits on a cliff while he watches a strange tower firing lightning bolts, and then rises to face against what it seemed to be members Ultra Brothers, Ultraman, Robot Zoffy, Ultraman Jack and Ultraman Ace. After incapacitating the ZAP SPACY's Space Pendragon, Ultraseven joined the group as they face against Zero.

Ultraman Saga opens with a powerful apocalyptic vision of Tokyo, buildings destroyed and the city seemingly devoid of life. We are soon introduced to the Earth Defense Force (EDF), Team U (played by members of the female idol group AKB48). They and a group of young children and the last survivors on planet Earth after the world was invaded by the evil Alien Bat, the rest of the human population having been abducted.