It's difficult to theorize with an almost total lack of information.
The common sci-fi "return to barbarism" theory (that the agents were human, who subsequently crashed on the Earth and forgot everything) doesn't go here because you've postulated that the war finished just in the last few centuries.
The ET theory requires the (largely unsupported by evidence) existence of local ETs. Technological artifacts on other planets would provide good evidence of this theory, but our presence on other planets is extremely limited, so this is a faint hope. Other evidence given on this forum (photographs of supposed buildings and monuments on other worlds) is generally not credible for a couple of reasons:
1) The size of the aforementioned structures is invariably on the lower limit of the resolution of the photograph, no matter what that is. So, we must accept that, for some unknown reason, ETs only built progressively larger and larger buildings the farther away from Earth they got, and smaller ones the closer they got.
2) The analysis of photographs is a skill - since a large amount of information that we are used to (from binocular vision) is normalized right out of a photograph, sometimes we see things as being different from the way they are when we only have a picture.
Like our old friend <a href="http://www.pacsci.org/traveling_exhibits/3-D/Images/triangle.jpg">the impossible triangle</a>, some things can fool your eyes when you only see them from one angle.
So, I am unwilling to accept the other photographic evidence of ETs at face value as it is presented here. As a result, if we want to demonstrate the existence of ETs to support this theory we'll need to find other evidence of their local presence.
If the ETs are the cause, then we are left with a few theories as to why the Earth would be spared in this system-wide war.
1) Earth is protected by some law - like a wildlife preserve or a sacred taboo
This is hard to believe, since I can't imagine what law would stand in such a war.
2) Earth is strategically unimportant to the ETs, so there weren't any here
Again, the rest of the system was attacked, and Earth doesn't have any special attributes that would make it less interesting for occupation.
3) They missed
If this were the case then there would still be ETs here, and again, no solid evidence has been produced that there are. They might concievably have left after the war, but that's really reaching.
What's the theory crater? I can't really think of a sensible scenario offhand that explains the present arrangement of things. Maybe you've got an idea.