What to do after catching rayquaza in emerald

1

Go to Sky Pillar, and press A in front of Rayquaza (who is at the top of the pillar).

2

Go to Sootopolis City. A cutscene should play.

When it's is finished, press A in front of Rayquaza (at the Sky Pillar again), and then go into battle.

Advertisement

3

Use level 80+ Pokémon (Rayquaza is level 70), and you should have 50+ Ultra Balls (or, if you still have it, your Master Ball), and then make Rayquaza fall asleep. Paralysis is also an option, but Sleep lasts longer.

If you have it, attack using False Swipe.

4

When Rayquaza's health bar turns red, throw Ultra Balls balls frequently. If you're using your Master Ball, you probably need to lower the health to about half, but throwing a Master Ball when Rayquaza's health is red will almost always capture it.