The aliens have come to destroy all life on Earth then restart it with new species that will be more acceptable to the other planets with their ultimate weapon, a massive space craft called Giga Endra. Justice appears at a meeting of top level EYES leaders to deliver a message from the organisation: In the near future life on Earth will become a threat to peace in the galaxy from the conclusion of the incident of Sandros (see 2nd movie). It is soon revealed that the mysterious woman Julie is Justice in disguise who has been sent by a Universal peace-keeping organisation called the Universal Justice to oversee their plans. Every attack is witnessed by a mysterious woman in black who shows no emotion and no desire to interact with any of the victims. With Cosmos out of the way the invaders begin an onslaught against the Earth's major cities.

It becomes apparent that these aliens don't want Earth's species to leave the planet. Cosmos is defeated by Justice and the aliens destroy the spacecraft that were to be used as transports for the monsters. Cosmos arrives in time to temporarily stop the attack when Ultraman Justice enters the battle aiding the alien invaders. While EYES prepare to safely transport the world's monsters to a far off planet where they will no longer be troubled by humans, an army of giant alien robots, called Gloker Pawns appear to stop the project.