一艘隶属美国的核潜艇在关岛附近消失,后经日本方面证实该潜艇已因事故遇难,而防卫军在调查过程中竟然还在海底发现巨大生物的存在。与此同时,新泻妙高山、鹿儿岛池田湖、小笠原诸岛等地接连发生强烈的地震和人员伤亡事件,关于50年前那头大闹日本的哥斯拉的恐怖记忆相继在人们的脑中复苏。 BS电视台女记者立花由里(新山千春 饰)近期正与同事调查接二连三的怪兽事件,从一个神秘老人的口中得知,所谓哥斯拉其实是太平洋战争中丧生的人们的冤魂聚集而成的怪兽,核潜艇事故引起的核泄漏似乎意外将哥斯拉唤醒。与它一同苏醒的还有被称为护国神兽的巴拉哥、摩斯拉、基多拉。日本本土面临空前的灾难……Strange incidents occur when an American submarine has been destroyed by a mysterious force at sea off the shores of Guam. Only Admiral Tachibana was certain that behind the disaster was none other than the destructive King of the Monsters, Godzilla! 50 years after his attack on Tokyo in 1954, Godzilla has mysteriously returned to life to destroy Japan, and General Tachibana, whose parents died in the monster's destructive wake, was prepared for his return to protect Japan from yet another tragic disaster, but is dismissed by the overly confident Japanese government, who underestimate Godzilla's power. But to further prove Tachibana's claim, his daughter Yuri, who works for the TV news program "Digital Q," investigates strange phenomena in three separate areas in Japan (two of which involve the deaths of immoral youths), and meets a mysterious old man named Isayama, who proclaims that aside from his infamous nuclear origins, Godzilla is an accumulation of vengeful souls (of both Japanese and non-Japanese) abandoned to die in the Pacific War, and thus, mere weapons cannot kill him. While Tachibana has now been vindicated by the government, Isayama awakens the Three Sacred Guardian Beasts of Yamato, which protected Japan in its ancient past, and were then put into hibernation in the aforementioned three areas of Japan. The three monsters, King Ghidorah (sky), Mothra (water) and Baragon (earth), fight the ravaging Godzilla, while Tachibana also prepares to go into battle against his old radioactive nemesis . . .