In 1968, the French government secretly carried out a nuclear bomb test on an isolated island in French Polynesia. This nuclear blast irradiated the egg of a marine iguana, causing it to mutate into a giant monster over the next several decades. When the creature, dubbed "Godzilla" by the American media, surfaced in New York in 1998, the French government sent a team of agents to the city to eliminate the creature and "clean up their government's mess." The team, led by Philippe Roaché, sought out Dr. Niko Tatopoulos, who had determined that Godzilla had laid eggs somewhere in the city. Together, Nick and Philippe's team of secret servicemen found hundreds of eggs inside Madison Square Garden, which hatched into Baby Godzillas that chased them through the arena. The other members of Philippe's crew were killed by the Baby Godzillas, but he, Nick and his girlfriend Audrey Timmonds and her cameraman Victor "Animal" Palotti escaped the Garden while the United States military delivered a missile strike on the building, destroying it and Godzilla's nest. However, the adult Godzilla soon rose from the streets and, enraged, gave chase to Philippe and the others. They hijacked a taxi and drove away from the beast, luring it to the Brooklyn Bridge, where it was entangled in the suspension cables and killed by three F-18 Hornets. His mission accomplished, Philippe returned to France.
Another French agent, Monique Dupre, was sent to New York to investigate reports of a surviving Godzilla. She discovered that this new Godzilla was being raised by Nick Tatopoulos, and placed a call to the U.S. military to destroy the monster. Godzilla was seemingly killed by the military, and Monique was then sent to Jamaica to investigate reports of another mutation that may have been born from the 1968 French nuclear test. There, she encountered Nick and his scientific team, H.E.A.T., who were also investigating the attacks, and offered her assistance. Eventually, they were attacked by the cause of the attacks, Crustaceous Rex, but were saved by Godzilla, who had survived the military's attack. Afterwards, Monique agreed to allow the new Godzilla to live, and was recruited as a member of H.E.A.T.
Philippe Roaché would later offer his assistance to the U.S. military on behalf of the French government when Godzilla was reportedly attacking New York. Philippe provided them with a deadly chemical weapon that he intended to use to destroy Godzilla. However, it was soon learned that the monster attacking New York was an impostor known as the Chameleon created to frame Godzilla by Cameron Winter. Philippe's weapon was used on the Chameleon instead, causing it to crumble into dust.
One day, Manda was travelling along the English Channel towards the United Kingdom. The Gotengo was launched, froze the ancient dragon, and then departed. Later, Kamacuras suddenly appeared in the French capital, Paris. The Earth Defense Force's French division deployed their aerial vehicle, Eclair, to battle the monster, but the battle was cut short when a UFO teleported Kamacuras away. The UFO's occupants, an alien race calling themselves the Xiliens, stressed that they had come to save the human race, but it was soon discovered they intended to conquer the Earth and enslave humanity. With their plan exposed, the Xiliens unleashed Kamacuras in Paris once again and destroyed the Eclair, leaving the city defenseless.
The monster Baragon, which had been burrowing underneath Europe for some time, finaly surfaced in the middle of France's capital city, Paris, destroying the Arc de Triomphe. The Counter-Kaiju Reaction Forces deployed their mecha, Kiryu, to subdue Baragon. After a fierce battle, Kiryu restrained Baragon and flew him to CKR's containment facility on the Monster Islands.