The Hoenn Region.
After receiving the "intelligence" Ye Li provided, Team Magma and Team Aqua did indeed find extremely important clues about Groudon and Kyogre at the seemingly unremarkable locations he had pointed out.
Deep beneath an active volcano, Team Magma discovered an energy altar covered in Ancient Runes. Its energy fluctuations closely matched Groudon's legendary aura.
Meanwhile, on the seabed of an area the Pokémon League had marked as "dangerous, uncharted waters," Team Aqua discovered the submerged ruins of an ancient civilization shrouded in a massive energy field. Murals within the ruins clearly depicted the legends of Kyogre.
These discoveries instantly brought Maxie's and Archie's trust in Ye Li, the mysterious "information broker," to its peak.
They began working even harder to provide all manner of assistance for the expansion of Ye Li's influence in the Hoenn Region.
Using this hard-won trust, Ye Li began laying deeper plans in the Hoenn Region.
While studying the region's ancient myths, he discovered an even more powerful being that both Team Magma and Team Aqua had overlooked, whether deliberately or otherwise.
A true overlord of the skies that stood above Groudon and Kyogre and maintained the balance between the heavens and the earth.
-Rayquaza.
Ye Li knew very well that if Giovanni's insane "Genesis Gate" plan succeeded, the disaster it unleashed would engulf the entire world.
When that time came, neither the Pokémon League nor Team Rocket, nor even the Groudon and Kyogre awakened by Team Magma and Team Aqua, would be able to remain unscathed.
To have enough say and the ability to protect himself in that world-shattering catastrophe, he had to possess an ultimate trump card capable of contending with Giovanni's "Genesis Gate."
Rayquaza was the final ace he had chosen for himself.
He secretly began using the intelligence network