Goro is sailing on a small boat in the waters off Japan earlier one morning when he notices a badly damaged fishing boat floating not far from him. Goro calls out to the ship hoping for someone to answer him, but no one responds. Goro climbs aboard the vessel, and finds it mostly abandoned.
As Goro moves further into the ship he finds several dead bodies, drained of all blood. Goro then discovers Hiroshi Okamura, one of the crew members, unconscious but alive, hiding in a locker. Goro is then attacked by Shockirus, the creature responsible for killing most of the crew. Okamura regains consciousness and stabs the Shockirus with a hatchet before it can kill Goro. Goro takes Okamura to his boat and asks him what happened. Okamura responds that a monster did this. When Goro asks if he means the giant sea louse, Okamura responds that there was something much bigger that attacked the boat first, but he could only see part of it.
Goro returns to the headquarters of the newspaper he works for in Tokyo to report his story, only to be told it is being censored by the government. When Goro asks his editor why, he responds that the government believes Godzilla destroyed the ship. Goro is instructed to speak to Professor Hayashida, a local scientist who is an expert on Godzilla. Goro visits Hayashida's lab, where Hayashida explains that Godzilla is a monster created by man, and is beyond the human construction of good or evil. At the lab, Goro meets Naoko Okamura, Hayshida's assistant, and learns that she is Okamura's sister. Goro decides to take Naoko to the hospital where her brother is being held, only to take photographs of their reunion, angering them both.
After the government reveals that Godzilla has in fact returned, Goro works with Hayashida, Naoko, and Okamura to find a way to stop him. When Godzilla comes ashore near a nuclear plant, Goro, Hayshida, and Okamura arrive at the scene and watch Godzilla feed on a reactor before suddenly leaving. At Hayashida's laboratory, they develop a plan to use magnetic waves to lure Godzilla into Mt. Mihara and imprison him under tons of molten magma. Okamura leaves to work with Hayashida's friend Dr. Minami in setting up the charges on Mt. Mihara. Hayashida, Naoko, and Goro prepare the magnetic transmitter to lure Godzilla, just as Godzilla arrives in Tokyo.
Godzilla nears the building and damages it, closing off the elevators and trapping the three. Fortunately, Okamura arrives in a J.S.D.F. helicopter and picks up Hayashida to take him to Oshima Island. The chopper is forced to leave Goro and Naoko behind, as the turbulence is too great. Goro and Naoko leave the building through the bottom, helped by a homeless vagabond who holds a rope allowing them to rappel down. Goro and Naoko reach the streets just as Godzilla destroys the Super X and begins approaching them. Thankfully, Hayshida activates the transmitter in time and Godzilla leaves for Oshima Island. Goro and Naoko, now attracted to each other after their ordeal, take a helicopter to Oshima Island and arrive just in time to witness Godzilla being imprisoned in Mt. Mihara.