It's reasonable to assume that many of the Ancients that we saw within Akadaemia Anyder and Amaurot were simply civilians, researchers and non-combatants. I suspect many of them could put up a decent fight if required, though we saw from above just how chaotic the situation happened to be. It's also a reasonable assumption that the second 'Final Days' is not going to be nearly as deadly as the first given that there wouldn't be much left of Eorzea or any of the other major regions if that happened to be the case.
The Ancients saw entire buildings crumble and collapse into dust. Horrific creatures emerge from thin air. Fire rain down upon them from the sky. Most importantly, though, the very fabric of reality began to unravel around them.