Ever since his first attack in Tokyo, the monster king, Godzilla has destroyed any Japanese city that lay in the path of his search for energies to fill his appetite. Soon, it became Japan's top national priority to develop a source of 'clean energy' that would not attract Godzilla. In 1996, the Clean Energy Factory led by Motohiko Sugiura (Masatou Ibu) developed a new plasma power generator in the metropolitan city of Osaka. Success seemed to be guaranteed - but, Godzilla appeared again, and demolished the entire power plant. Members of a special combat unit risked their lives in this doomed fight. One of the members, Kiriko Tsujimori (Misato Tanaka) tried to load shell in the rocket launcher. But while she was desperately trying to stop her hands from shaking, her much respected commander - Takuya Miyagawa (Toshiyuki Nagashima) lost his life under the falling concrete debris of the power plant.

Now, it is the year 2001 and Kiriko leads the 'G-Graspers' - a special anti-Godzilla unit in the 'G-Command', a new division created in the Ministry of Defense after the destruction of Osaka. Now her sole purpose in life is the extermination of Godzilla. She has powerful support from a physicist, Yoshino Yoshizawa (Yuriko Hoshi). Their plan is to wipe out Godzilla completely, as simply killing him would merely create a hazardous radiation leakage. The best solution, therefore, is to create an artificial 'black hole' which will suck in everything into another universe. The difficulty is to reduce the size of the weapon to 2 meters in diameter - a size small enough to be carried on a satellite. A young inventor has the answer. Hajime Kudo's (Shousuke Tanihara) long and hard working days produce the ultimate weapon: the Dimension Tide.

Tests continue on the operation of the man-made black hole. One day, Yoshizawa and the team accidentally cause a black hole which creates a distortion in the time dimension. An uninvited intruder comes through this hole. An ancient giant larval Meganulon, which finds a new home in modern Japan. Meganulons need water to grow, so they find water veins under the city of Shibuya. They break the water veins, flood the city and use this newly formed lake in Shibuya to multiply and grow. As the swarm grows, humans become their favorite targets. But this was only the beginning. As the Meganulons metamophose into adult Meganulas, they are attracted by Godzilla's enormous power. They attack Godzilla in order to suck in his energy and inject it into a special larva wich will cause it to become a gigantic dragonfly - a 60 meter long Megaguirus!! It is now Megaguirus's turn to attack Godzilla to devour his energy.

A three-way battle between Godzilla, Megaguirus and humans!
The battle for survival in Odaiba!
Can humans really exterminate Godzilla?
And....... is there a future for Japan!?