I got out my DVD (I just love working graveyards and not being able to sleep on my nights off
) and watched the alternate ending to "Powerless" just now. I agree that the virus spreading would have been a powerful storyline as it played out. I liked Nathan collapsing to start off the epidemic, which would have motivated Peter to do whatever it took.
I definitely like the storyline planned for Peter and Nathan for next season, though. Definitely.
Pasdar and Ventimiglia's dynamic will lend itself to the emotional stakes big time.