Towards the end of Pokémon Omega Ruby and Alpha Sapphire you will have a couple of story driven Delta Episodes with Zinnia and they will be kind of awesome.
First off, you get to ride Rayquaza. Second, you go into space and battle Deoxys (with Rayquaza).
The Deoxys event is optional, but there's really no reason not to do it. The Rayquaza you encounter is level 70 and will require tons of Poké Balls, HP restoring items and your best Pokémon party. When I say bring tons of Poké Balls and HP restoring items, I mean it. Right after you fight Rayquaza you jump into battle with Deoxys, come prepared.
Without further ado, here's how to grab these two:
Rayquaza
Rayquaza is actually a part of the storyline, you will encounter it during a Delta Episode at the top of the Sky Pillar with Zinnia. Rayquaza will be level 70 when you encounter it and in order for you to proceed with the game, you must capture it.
On the top of the Sky Pillar you will awaken Rayquaza, Zinnia will be looking to act as Rayquaza's protector – but instead it will eat your meteorite and challenge you. Remember to take HP restoring items with you on this journey, as you will be needing them. After Rayquaza challenges you and you capture it, send a Pokémon back to your box so that Rayquaza can join your party. Once it is in your party Zinnia will teach it Dragon Ascent and challenge you to a battle.
Dragon Ascent will allow Rayquaza to Mega Evolve without a Mega Stone.
Deoxys
Defeating Zinnia (after capturing Rayquaza) will launch you into space, literally.
Rayquaza will fly you into space for you destroy an asteroid that is heading towards the planet. Rayquaza will Mega Evolve to destroy the asteroid, but the asteroid isn't actually defeated — that's because it's actually Deoxys.
Deoxys is Level 80, beware.
