I think storyline could be something like this:
N will release his Zekrom/Reshiram and let it back to Unova. He was constantly releasing his Pokemon during B/W, so this time he might do that as well.
In Black 2 you meet Hilbert having Reshiram he caught in original Black. In White 2 you meet Hilda having Zekrom she caught in original White. At some point of storyline you and Hilbert/Hilda would must go to encounter Kyurem. Before you go, N's released Zekrom/Reshiram would attack you. At this point it will be required to catch that Zekrom/Reshiram in the same way like in B/W.
After you and Hilbert/Hilda go to Kyurem, Ghetsis would appear and challenge you to battle. Hilbert/Hilda will accept challenge and fight with his/her Reshiram/Zekrom. In the meantime you encounter Kyurem. During battle with Kyurem your Zekrom/Reshiram would fuse with Kyurem (see my entry in alternate form thread to see how it would be done). After catching new Kyurem's form, you will see that Hilbert/Hilda lost battle with Ghetsis and you would must to defeat Ghetsis with your freshly caught Black/White Kyurem.