PokéBase - Pokémon Q&A
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I'm sure there's a limit of how many boxes you get.

Does anyone know what happens? Like Reshiram/Zekrom, does it just go somewhere else to be caught later, or does it just faint and you can't get it again or...?

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I have no source to confirm this, but this is probably right.

Apparently, when you engage in a battle with Xerneas/Yveltal, regardless of whether you defeat it or catch it or whatever, a new Box 31 will be created in your PC.

So, really, there is no way your entire PC can be full of Pokemon, the captured Xerneas/Yveltal will just go to the newly created Box 31.

Hope I helped. :)
Source

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The boxes reach a certain limit tho
...What? Box 31 is a brand new, legal box. 31 is basically the limit.
What if box 31 is filled?
I just said it was a brand new box that is unlocked when you battle with Xerneas and Yveltal.
Oh :P (filler)
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You can catch the Pokemon but you are not allowed to keep it, sorry.
Hope I helped!

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