In Japan, a team of scientists led by Yuji Shinoda, along with his daughter Io and reporter Yuki Ichinose, are investigating Godzilla, who has re-emerged from the depths of the ocean. The trio belongs to an organization called the Godzilla Prediction Network (GPN), which is dedicated to studying and predicting the movements and behavior of the colossal creature. As Godzilla surfaces and begins to wreak havoc across the city, another group known as the Crisis Control Intelligence (CCI), spearheaded by Mitsuo Katagiri, seeks to destroy Godzilla using advanced military technology. A clash of ideologies ensues between the GPN, which believes in understanding Godzilla, and the CCI, which views annihilation as the only solution.

As this conflict unfolds, an ancient UFO is discovered underwater. The UFO suddenly activates and takes to the skies, revealing its disruptive intent by making wireless communication inoperative across Japan. Both the GPN and CCI converge on studying this new threat, only to uncover that it harbors a malevolent alien life form which has come to Earth with its own agenda. This alien entity attempts to use Godzilla's regenerative properties for its own fiendish purposes, leading to an intense and catastrophic struggle. With Godzilla's unpredictable nature and the emergence of this extraterrestrial menace, humanity finds itself facing unprecedented peril.