^As I said, it was the only piece of footage from what would have been episodes 2x12 and 2x13 that had a "SPOILER ALERT" caption.
There were other scenes that Tim Kring says cannot be repurposed as they've decided to go in another direction now.
This part is not a spoiler. In the alternate ending the Nikki, Monica and Micah and Sylar cliffhangers are the same. Nikki still gets blown up and Sylar still regains his powers. In addition, Hiro still buries Adam alive.
My non-spoiler guess with Nikki is that Jessica resurfaces which reactivates her powers and allows her to escape.