2014 yapımı Godzilla'nın devamı niteliğinde olan filmde, kripto-zoolojik bir kuruluş olan Monarch dünyanın çeşitli yerlerinde buldukları kadim yaratıkları izlemeye devam etmektedir. Ancak hükümetler 2014 yılında ki olaydan sonra bu kadim yaratıkların tamamen yok edilmesini istemektedir. Efsane oldukları düşünülen bu kadim süper türler bir anda tekrar uyanır ve birbirlerine üstünlük kurmak için savaşmaya başlar. Bu savaş insanlığı yok olmanın eşiğine getirecektir.
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.
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.
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.
The fairies from Infant Island discover a lost city, as well as a giant monster that is attracted to environmental calamities.
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.
A young pilot narrowly escapes the destruction of her home in a stolen ship, only to be followed by the colossal cockroach responsible.