Save the game when you get to Rayquaza then get loads of ultra balls and make Rayquaza's life down to red and use the ultra ball (theres a ball that you can use when the opponent life is red but i dont kno what the ball is called cuz i forgotten) You can use that too but i dont kno if it works Well,
Good luck!
And get Catching!
Master Ball
Try to get a ultra ball
You could if you were to damage Mewtwo or cause status problems to him... I recommend a Ultra Ball.
Since Mewtwo is in a cave, try using Dusk balls. If it doesn't work, Master ball. If you already used the Master ball, then buy as many Dusk balls as you can and try to catch it. If your patient enough, try catching Mewtwo with full health.
from 1HP to 10 or 15HP. I highly suggest using a Master ball.
You can catch Mewtwo easily by using a Master Ball on it or by using an Ultra Ball on it after lowering its HP.
since you're in a cave,i could recommend a dusk ball.
I prefer to use my Master Ball for Mewtwo, but at least use an Ultra Ball.
Master Ball
You can probaly catch him with a ultra ball but I would use the master ball
master ball ultra ball quick ball or a premier ball
With a master ball.
Throw a Master Ball at it.
Well it matters what game you have, if you have Pokemon fire red, you can catch it with a master ball
to catch suicune,mewtwo,raikou and entei
The only sure way to instantly catch any Pokemon is with a Master Ball.
a master ball preferably but any ball will work with a bit of luck