I appreciate that you just called out for this.
The key is the FBI evacuating everyone. That most likely means not a physical danger, but an information danger. Either a foiled terrorist attack (but why?) or the disovery of information that will be bad for Earth - pick your poison.
Asteroid imminent impact, while a fan favorite, isn't going to work Because that place is neither the best location for that work, nor the only telescope that can spot Earth Killers. Still could be, however, if they were the first to find. However, why make a big deal of it? With a physical presence people are going to be suspicious, like we are now. Why not just take the entire staff quietly, at their houses?
One big item, still falling under the information discovery, is that we have a major solar storm coming our way, one that we might not weather so well. Not sure if a big enough solar ejection can really harm the earth or not, but I would guess that it could, if it was big enough.
Seriously though, probably aliens.