Aquapolis was before Atlantis came to be on the surface. Thousands of years ago, when Atlantis was first formed, Aquapolis and Skyridge teamed up as Atlantis had too many powerful Pokémon that could wreak the planet and they had to destroy it.
But they went to war after the Atlantis destruction. Aquapolis believed Skyridge was too visible and if it was to be found, then surely Skyridge would have no need for the mystical force holding it to the air, and it would collapse and destroy Kanto.
But the Skyridgians don't want this. No. They want Aquapolis to be destroyed.
Do you want to join Aquapolis? Great!
Just tell Aquapolis your deck and you're ready to go!