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Used on Dialga b/c my pokes were weakened already and couldnt battle although i had alot in emerald after using mod shop cheats and inf cash so i migrated some later after i got the national dex to catch the rest of my pokes, I dont really bother with battling as much as i do collecting and ev training/breeding.
I usually avoid using my Master Ball in every game that I have, just to be on the safe side. I might use it on Arceus though, if I get the Heaven's Pipe. (What am I thinking?)