In a universe where the Cold War never ended and growing conflicts result in the rapid advancement of technological warfare, the cyborg spy Mylene Hoffman of the 00 Organization battles the agents of the Eastern block in a game of high tech espionage.

In the beginning of the movie, 20 years ago, on the moon, the 4 Ultra brothers, Ultraman, Seven, Jack, and Ace were fighting a deadly foe known as Yapool, a monster that was several times their size. As they fought, Yapool had a clear advantage and used his several claws to grasp the brothers, although, they managed to clear from the claws through there powers and used a combined Specium Ray to no avail. The monster then flies off to Earth to dodge the attack and the brothers follow. The brothers were barely able to defeat Yapool but the monster still needed to be sealed. However, to seal Yapool away they were forced to give up the ability to transform, and took up jobs to be in the area of Kobe in case the monster ever returned.

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?

A young boy discovers a magical rock that can make any wish come true. But the rock is stolen by a school bully who uses it to create a powerful and dangerous monster. The only way to stop the beast is to enlist the help of superhero Ultraman Gaia. The boy does everything he can to help the XIG Team, a brave group of humans who have direct contact with Ultraman Gaia as well as Ultraman Dyna and Ultraman Tiga.

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.