Well, this old chestnut will run and run and is usually good for at least one blockbuster or 3, depending on how you spin it out. You get all the old favourites:

1. They arrived circa Roswell, 1947 and things went downhill from there.
   
2. They were or heavily influenced the "Atlanteans" or some other ancient civilization. Take your pick.
   
3. More than one species has been here at different times pursuing different agendas. Keep your Von Danniken books handy.
   
4. They were the various influential religious, political, cultural leaders, gurus, saints, geniuses, etc., who made their mark and had an irrevocable influence on human history.
   
5. The aliens did the dirty on the dinosaurs 65 million years ago. Bad for the dinosaurs, but good for us. Where does that one put us???
   
6. Our dear planet is a distant colonial outpost in some galactic empire in which we're little more than the "indigenous native primitives". Explains why all governments are so heavy-handed, crass and oppressive, no matter what sort of ideology/philosophy they profess. They're just badly-organized aspects of a divide-and-rule colonial administration with policies set in motion by someone who doesn't really have a feel for life as we humans live it.
   
7. Our planet and solar system is little more than a minor piece of territory in a vast galactic turf war between various species who are slugging it out for the post of top banana.
   
8. Was Hitler and his band of moral defectives set up by aliens as part of an experiment on their part?
   
9. Why are there constant references to "all-powerful beings from beyond" in so much of our mythology & religion? Is it all just so much forelock tugging deference to some bunch of conceited ET's?
   

        Right-o from a story point of view, if they're here, what's in it for them? Are they advance scouts for an expanding empire? A military outpost? Asset stripping this planet (as in the film "V". Not too likely as things haven't gone that far downhill. Yet…)? Amusing themselves by manipulating us like so many chess pieces? It goes on and on.

        One of my pet themes is that our section of the galaxy is a "wilderness reserve" of some sort. Explains why we never find any evidence of ET cultures. They're blocking all transmissions into this sector in order to keep it "unpolluted". Also explains all the weird ET encounters. They're just the tourists in the park.