The members of the Super GUTS force, one of whom is secretly Ultraman Dyna, are in the middle of a losing battle against an enormous monster on the surface of the moon, when suddenly a spaceship appears and saves them by zapping the beast. The crew of the ship claim to members of the world peace force that originally created the Super GUTS force, and they invite the GUTS members to enter their brainwave patterns into the ship's battle computer so it can be a more effective fighting system. It sounds like a good idea, but could they have some other plan up their sleeves?

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.