>>53339491"My people know it. From generation to generation, we pass along the lore about the distortions in the world borne by the Mega Evolution mechanism. And about the existence of another world, which we have long observed to be just like this one and yet not the same... That's right. A Hoenn region that's almost exactly like this one we live in. Filled with Pokémon and people like us. A world where maybe the evolution of Pokémon took a slightly different path, where Mega Evolution is unknown... A world where that war 3,000 years ago...never happened. A world where the ultimate weapon was never even built.”
- Zinnia, ORAS
"Let's talk about Mega Stones briefly."
"My theory is that they're special stones irradiated by the light--the energy of the Legendary Pokemon Yveltal/Xerneas--fired from the ultimate weapon 3,000 years ago."
- Sycamore, XY
Plus AZ’s cutscene shows that the energy beam differs between each version - blue (X) and red (Y) - on top of version exclusive stones also being named either X or Y.
Rayquaza could only Mega Evolve because of the weapon - Xerneas or Yveltal’s energy - being fired 3000 years ago. That energy shot up into space (AZ cutscene) and made contact with meteorites in the stratosphere, the ones Rayquaza ate.
That same energy is also why Primal exists.