Well here's an idea.
Godzilla is disturbed by a nuclear submarine and attacks the mainland, destroying everything in his path. A scientist begins work on a weapon to kill Godzilla, which is dubbed the Oxygen Destroyer (please note, this one is NOT in the original timeline) that is composed of microorganisms that consume oxygen, producing a lethal byproduct that dissolves anything organic in contact with it. As Godzilla continues rampaging, the military deploys special freezing bombs containing liquid nitrogen, managing to put him in hibernation. But while they debate what to do, the scientist's experment is tested and dissolves a tank of fish, but he's startled to discover that a hole is cut in the side of the tank the next morning and the tank has drained completely.
Several hours later, the security guards at the lab and personal are attacked by human sized monsters, which are discovered to be the Oxygen Destroyer chemical having taken on a life on if its own, gradually mutating. As the military tries to kill the creatures, they merge together into one giant creature dubbed Destoroyah, which begins destroying everything in its path, normal troops unable to get in range due to the toxic byproduct gas being present within range of the monster and any serious damage inflicted is healed by him breaking down and reforming. It's discovered Godzilla's regeneration would render him immune to the gas and the military is convinced to thaw out Godzilla to fight Destoroyah.
Godzilla and Destoroyah fight and Godzilla is badly wounded in the fight, but continues to battle. The scientist, guilt ridden he created Destoroyah, takes a craft full of the freezing bombs and drops them on Destoroyah, weakening him but being killed by Destoroyah in the process. However, now weakened, Destoroyah is overpowered by Godzilla and killed by having Godzilla's Atomic Ray fired through his now brittle body, blasting a gigantic hole through his chest before he can break down and heal. Godzilla, battered from the battle, returns to the see.