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I'm starting the Delta Episode, and, since I'm planning on using my Master Ball on Deoxys (Unless it would be better to use it on Rayquaza, would it?) what would be some good balls to use? I already came up with using a Quick Ball at the start, just in case I get lucky, then using Dusk Balls (I'll specifically start the cutscene at night so they'll have full effect) Timer Balls, for if it takes a while to bring him low, and of course, the heavily used Ultra Ball. Any other ideas, am I missing some vital ball that could help a lot, or did I cover everything? Also, please include if I should use my Master Ball on Rayquaza, or Deoxys like I had originally planned.

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You should use your Master Ball on Deoxys. It's frail, and if you KO it, you have to restart the entire cutscene. Your current setup is good -- start with Quick Ball, fling Dusk/Ultra Balls until Timer Ball bonus takes effect, then use Timer Balls. I don't see anything to be improved upon, just get lucky.

Hope I helped!

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Whatever you do, DO NOT USE YOUR MASTER BALL ON RAYQUAZA. Since you need rayquaza to fight deoxys, it will always respawn until you catch it. As for whatever ball is the best to use, I don't know, I guess it doesn't really matter since you need to catch it, anyways.