They give the one that version is for to N, the second to final battle it is used by N. You get the opposite of what N has. In Pokémon black, N has Zekrom, and in Pokémon white, N has Reshiram. This is changed in Pokémon Black 2 and Pokémon White 2 which takes place sometime later and now Ghetsis has obtained Zekrom in Black 2, and Reshiram in White 2 (probably stolen from N) and attempts to use them with Kyruem in an attempt to kill the player.
