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Put him to sleep or freeze him, then weaken him down to the point where you can barely see the red and catch him with an Ultra Ball or another high end PokeBall.
The best idea is to use a move like False Swipe so you're 100% sure he has one HP afterwards. Then you can put him to sleep or freeze him. After that you should use a Great Ball or Ultra Ball and press B up when the pokeball opens. (Sometimes this helps catch a Pokemon)
Or....
Use Mareep or any other Electric and/or poison type to paralyze him and then use Cotton Spore. You can then lower his health and attempt to catch him.
If you've already dealt with the scene at Sootopolis City then you can capture him. The way I did was to first find the master ball in team aqua's hideout at Lilycove City. Once you're at the top and start to battle with him do try and lower it's Hp (even though your going to use a master ball). Fire and Fighting types don't work very well so don't use Blaziken. Once you've lowered it's HP use the Master Ball and it will be yours.
The Master Ball will catch any Pokemon on the first go. However, Rayqaza does not require this as he can be caught with an Ultra Ball or lower powered ones. It is recommended to save your Master Ball for a Pokemon that cannot be caught with regular balls like Latios and Latias. Just paralyze him, and lower his health with moves, but be careful not to make him faint. You should use your Pokeballs and Great Balls first as this helps with capturing him. Then just use tons of Ultra Balls until he gets captured.
Raquaza will only appear at Sky Pillar.
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What do you do after beating the elit four?
GO to route 130 , and catch Rayquaza. GO to route 130 , and catch Rayquaza. GO to route 130 , and catch Rayquaza.
Where to catch Rayquaza on Pokemon Indigo?
You can catch Rayquaza in the map called "Blackthorn City".
How do you catch Rayquaza in crystal?
Rayquaza isn't in Crystal.
Can you catch Rayquaza in Pokemon Black?
No, you cannot catch Rayquaza in Pokémon Black.
How do you get Rayquaza on dimand version?
You cannot catch rayquaza in diamond
How do you catch Rayquaza in xd?
Rayquaza is not avaliable in Pokemon XD
How do you catch Rayquaza in Pokemon Black?
You cannot catch a Rayquaza in Pokémon Black, you will have to either transfer it from a previous game or you can also trade with someone for a Rayquaza.
Can you catch Rayquaza?
Yes.
How do you catch Rayquaza platinum?
no
Do you need to catch Rayquaza?
It is not necessary to catch Rayquaza. It's an optional legendary Pokemon that you can find at Sky Pillar.
Where to catch a Rayquaza in FireRed?
You cannot catch rayquaza in fire red you must trade from either ruby or sapphire.
What ball to catch to catch Rayquaza?
Ultra ball.
