So the aliens they are going up against are like the wraith in Atlantis? There was at first a small force to watch over the sleeping ones.
Sure, why not. Anything is possible. But scenarios that make the aliens more powerful are a problem because, where does the story go with that? The aliens are already more powerful than the militia can handle. Even if they destroy the ship over Boston, there's going to be many more across the globe just like that.
The fight is too one-sided, which is why my hunch is that, whatever the big twist coming up turns out to be, it will be something that equalizes the fight more, while increasing the complexity. That's how they'll be able to keep the story going without it becoming a repetitive bore.