I have not played Mass Effect 3 yet but do not care of spoilers, so spoil away for me if you have an answer to this.
If the Reapers have been slumbering for 50 thousand years, and they are 50 thousand light years away in the deep space of the galaxy like it lays out in Mass Effect 2, then why don't we see them when they were active? The light that astronomers would have been observing would be 50,000 years old by the time of the trilogy, and if there was a mass extinction event, those astronomers would have observed it.
Any sort of war on a galactic scale would have dispelled enough energy to make it observable in the sky.
Is there any story justification for this in 3?