What Will Happen to it?

[Strdstwanderer]

hypothetically speaking if you have all 649 pokemon in your PC Box (as in One of every pokemon in your PC box) and you have 6 more pokemon along with you (say that you have 2 Swellows one in your PC and one in your Team) What will happen if you capture a new pokemon? where will it go? and What would happen if you also have a pokemon in the Dream World then you Woke it up where will it go? or in HG/SS where will the pokemon from the Pokewalker Go?

 

[Pyrax]

The storage system has enough space for 720 pokémon.
And even if you did have 720 pokémon in the box and 6 pokémon in your party, then you wouldn't be allowed to catch more pokémon until you release something.