Taking place after Godzilla: Final Wars, the film starts with Godzilla and Minilla living in peace on Monster Island. Suddenly, an explosion is heard and Godzilla goes to investigate, leaving behind Minilla. Godzilla discovers a strange machine. The machine opens up and releases a small arm-like claw with a DNA scanner on it. The machine attempts to Godzilla, but Godzilla quickly destroys the machine with his atomic breath before it can. Godzilla looks up into the sky, and sees a few more scanner machines flying above him. They all land in different areas on the island, and Godzilla goes to investigate more. Meanwhile, a spaceship lands on the Moon, and an astronaut comes out and looks around. He pulls out a device. The device starts beeping loudly, and the astronaut, concerned, turns around to get back on the spaceship, when suddenly, a giant Xilien robot comes crashing through the ground. The Xilien robot picks the astronaut up by the neck, and throws him into the Sun. The robot turns around and picks up the ship, then crushes it with it's bare hands. The robot looks at Earth, and flies toward it. Halfway to Earth, the robot stops and sends a message to it's controllers, the rebel Xiliens, telling them that it's almost there. The robot continues flying towards Earth. Meanwhile, in Japan, a scientist named Akatsuki and his assistant, Amaterasu, are informed of the mysterious disappearances of the astronauts who recently landed on the moon. The two theorize about what it could have been, when suddenly the giant Xilien robot lands in the middle of Tokyo. It begins wreaking havoc, when suddenly it is shot with missiles by several helicopters. The robot activates it's laser cannon and destroys the helicopters. The robot continues destroying the city, as Akatsuki and Amaterasu try to think of a way to stop it. Back on Monster Island, Godzilla runs into Kumonga, who seems a little stranger than usual. Godzilla fights Kumonga, and, after a long battle, defeats him. Godzilla throws the defeated Kumonga into a tree. As Kumonga hits the tree, some sparks shoot out of a machine stuck on his head. The machine falls off as Kumonga falls and hits the ground. Kumonga gets back up and scurries away. Godzilla, confused, continues walking. After a while, Godzilla runs into a confused Anguirus, who is being scanned by one of the machines Godzilla saw flying in the sky earlier. As the scanning stops, the machine shoots a small device at Anguirus's face, which sticks. Anguirus tries to get the device off, but suddenly some sparks shoot out of it, and Angurius stops. Godzilla takes a few steps forward, only to be tackled by Anguirus. Godzilla shoots Anguirus into the sky with his atomic breath. As Anguirus is soaring through the sky, Godzilla picks up and throws a tree at him, knocking him out of the sky. Godzilla goes to see where Anguirus landed. Back in Tokyo, the giant robot is attacked by some army tanks. The tanks shoot missiles at it, but the missiles don't work one bit. The robot's torso opens up, revealing a huge machine gun-type weapon. The robot shoots the tanks with the weapon, destroying them. The robot's torso closes, and it continues it's rampage. Meanwhile, Akatsuki and Amaterasu begin building a weapon to defeat the robot, when suddenly, the building they are in is destroyed by the robot's laser cannon. The two scientists survive and run for their lives as the robot continues destroying the building. The two scientists safely make it to a building full of other survivors. They take a seat, and show some others their blueprints for the weapon they were going to build to defeat the robot. Somebody tells them they should show their idea to the government, so the two decide to get out of the building, tell one of the soldiers, and see what they can do. The two run out of the building, but are nearly killed by the robot's laser cannon. They survive, but end up in an empty building. Back on Monster Island, Godzilla, still looking for Anguirus, is attacked by Ebirah. He notices that Ebirah has one of the smalll devices stuck on his head, like Kumonga and Anguirus did. He tries ripping the device off of Ebirah, but Ebirah seems more powerful than usual. After a long fight, Godzilla finally blasts Ebirah's head off with his atomic breath, winning the battle at last. Suddenly, a loud crash noise is heard, and Godzilla goes to see what it is.