My reasoning for this is simple, when Emmy sent back Mecha-King Ghidorah, she inadvertently causes Japan to become the corrupt superpower that the EEE wanted to prevent from happening. Let me explain:
- When Mecha-King Ghidorah was defeated and left to sink in the ocean, his remains were salvaged to create the Garuda and MechaGodzilla.
- When those were trashed, their remains were used to build M.O.G.U.E.R.A. (which consists of the Star Falcon and Land Moguera).
- These machines were some of the most powerful in the Godzilla franchise (MechaGodzilla paralyzed Godzilla and Godzilla needed M.O.G.U.E.R.A.'s help to defeat SpaceGodzilla when he usually would fight alone).
These machines were built from future technology. I believe that reverse engineered technology from the future propelled Japan decades ahead of the rest of the world in terms of technological advancement. This gave Japan an advantage and made it probably the most powerful country on Earth in the future. And all because Emmy didn't bother cleaning up after herself.