Follows the heroic efforts of the crypto-zoological agency Monarch as its members face off against a battery of god-sized monsters, including the mighty Godzilla, who collides with Mothra, Rodan, and his ultimate nemesis, the three-headed King Ghidorah. When these ancient super-species, thought to be mere myths, rise again, they all vie for supremacy, leaving humanity's very existence hanging in the balance.
Searching for his brother, Ryota stows away on a boat belonging to a criminal alongside two other teenagers. The group shipwrecks on Letchi island and discover the Infant Island natives have been enslaved by a terrorist organization controlling a crustacean monster. Finding a sleeping Godzilla, they decide to awaken him to defeat the terrorists and liberate the natives.
At the turn of the century, all of the Earth's monsters have been rounded up and kept safely on Monsterland. Chaos erupts when a race of she-aliens known as the Kilaaks unleash the monsters across the world.
Journalists Ichiro Sakai and Junko cover the wreckage of a typhoon when an enormous egg is found and claimed by greedy entrepreneurs. Mothra's fairies arrive and are aided by the journalists in a plea for its return. As their requests are denied, Godzilla arises near Nagoya and the people of Infant Island must decide if they are willing to answer Japan's own pleas for help.
Shipwreck survivors found on the presumably uninhabited Infant Island leads to a scientific expedition that discovers a surviving native population along with the Shobijin, tiny twin fairy priestesses of the island's mythical deity called Mothra. After the fairies are kidnapped by an exploitative businessman named Clark Nelson, Mothra sets out to rescue them.
To save the world, Mothra goes back in time in an attempt to defeat a younger King Ghidorah.
A new Mothra takes to the air and battles against Desghidorah to save all of humanity.
The fairies from Infant Island discover a lost city, as well as a giant monster that is attracted to environmental calamities.
A young pilot narrowly escapes the destruction of her home in a stolen ship, only to be followed by the colossal cockroach responsible.