Pacifidlog town is west of Route 131, and is encountered later in the game than most areas. [1] X Research source
You can get Rayquaza either before or after the Elite 4, it is your choice.
If you haven’t gotten this far in the quest, you can’t catch Rayquaza. [3] X Research source
The Sky Pillar stages are filled with strong Pokemon, but they can be avoided if you use a Max Repel. This is a good way to save your Pokemon’s HP for the big battle with Rayquaza later.
If you’re throwing the Master Ball, toss it out on the very first turn. It will capture Rayquaza automatically for you!