French nuclear tests irradiate an iguana into a giant monster that viciously attacks freighter ships in the Pacific Ocean. A team of experts, including Niko Tatopoulos, conclude that the oversized reptile is the culprit. Before long, the giant lizard is loose in Manhattan as the US military races to destroy the monster before it reproduces and it's spawn takes over the world.

Humanity finally rids themselves of Godzilla, imprisoning him in an icy tomb in the South Pole. All is peaceful until various monsters emerge to lay waste to Earth's cities. Overwhelmed, humanity is seemingly saved by a race of benevolent aliens known as Xiliens. But not all is what it seems with these bizarre visitors. If humanity wishes to survive, they must reluctantly resurrect their most hated enemy, Godzilla.

Godzilla has become a distant memory for Japan when the destruction of a US submarine raises alarms for Admiral Tachibana. His estranged daughter Yuri investigates the legend of the guardian monsters, who must rise to protect Japan against the vengeful spirits within Godzilla that seek to destroy both the nation and its people for the suffering they inflicted in the Pacific conflict.