Mining engineer Shigeru investigates the disappearance and death of his fellow coworkers when prehistoric nymphs are discovered emerging from the mines. After an attack on the local village, Shigeru heads deeper into the mines only to make a more horrifying discovery in the form a prehistoric flying creature. Soon a second monster appears as the two converge in Fukuoka.
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.
In Japan, scientifically advanced invaders from the war-destroyed planet Mysteroid cause an entire village to vanish, then send a giant robot out to storm the city by night, after which they request a small patch of land on Earth and the right to marry earthling women, claiming to be pacifists. Mankind must decide whether to capitulate or to resist.
