Do you have to use your Master Ball on Zekrom, or do you technically already
'own' him?
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You don't own him you have to catch it just like any Legendary but my advice is that you shouldn't use the Master Ball on him since it seems to be pretty easy to catch without it. I did catch it with just one Ultra Ball but in my case his HP were really low, probably 1HP left. You should use the Master Ball on the Pokemon that goes around the region so you don't have to be looking for him all the time.
I used my Master Ball, but using it on the roaming legendary is advisable. I, personally, am going to get the second Master Ball as a reward from 50 trades/transfers. (I have a stack of Pokemon lying around in my Pearl/Diamond/HeartGold PC boxes)
I caught him with a regular poke-ball without killing any of it's life
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