Godzilla is a 170-foot tall, radioactive, fire-breathing monster who's once again arisen from the seas off Japan, apparently intent on destroying all sources of energy across the land. Yuji Shinoda (TAKEHIRO MURATA) is a scientist who, along with his young and precocious daughter, Io (MAYU SUZUKI), and tag along local photographer Yuki Ichinose (NAOMI NISHIDA), is intent on studying the beast.
Unfortunately for him, Mitsuo Katagiri (HIROSHI ABE), the head of the Crisis Control Agency, wants to destroy Godzilla due to the path of death and destruction the monster weaves whenever he comes ashore. Katagiri's attention is divided, however, between Godzilla and what appears to be a large and ancient meteorite that's been discovered on the sea floor.
Along with his associate, Shiro Miyasaka (SHIRO SANO), Katagiri wants to know about the large rock, particularly when it begins flying around the city, scanning both the molecular structure of every creature it meets - including Godzilla - as well as the contents of a large city's computers.
Things become more complicated when the flying rock seemingly joins the Japanese military's attack on Godzilla and then spawns a similarly monstrous-sized creature. From that point on, it's a battle of the monster heavyweights as Godzilla and the alien creature go toe-to-toe and end up destroying much of the city during their epic battle.