三頭龍王者基多拉從地底長眠中甦醒，並召喚隱藏在世界各地的巨大怪獸，使全球陷入末日毀滅危機。長期蟄伏在深海底的哥吉拉，也感受到基多拉的邪惡力量，於是回到地表正面迎戰基多拉，為地球的霸權而戰…
良太一直想要找到一艘船前往南海去尋找失蹤的哥哥彌太，某天良太參加一場比賽，而那場比賽第一名的獎品正是一艘遊艇，但是卻因為報名時間已過而徒勞無功，不過良太卻在因緣際會下結識了市野和仁田，三人一同到港邊去看遊艇，結果在其中一艘遊艇上遇到了搶劫犯吉村，而急著尋找自己兄長的彌太便趁著其他三人熟睡時將遊艇開出，結果在海上遇到暴風雨，遊艇還遭到不明物體的攻擊而沉沒，四人及時逃生而逃過一劫，大難不死的四人漂流到一座島上，在那座島上四人發現了海裡有龍蝦怪獸伊比拉，然後島上有個叫做紅竹的神秘組織，而紅竹似乎在島上進行著一項不為人知的計畫，四人正巧碰上了一位從紅竹手下逃脫的一位女原住民，在那位女原住民的幫助之下四人潛入紅竹的基地，沒想到卻誤觸警報，良太在驚慌之中抓住了一個氣球往天空飄去，其他人為了逃避紅竹的追捕於是逃到了一個山洞，沒想到他們發現了哥吉拉正在那個洞裡面沉睡著...........
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.