The Fallen's agenda - at least as far as anyone not working for Bungie development staff know, anyways - basically consists of three things:
-Kill a lot of stuff.
-Steal a lot of stuff.
-Take back the Traveler.
As far as anyone can tell, the Fallen weren't always what they are now (nomadic, brutal scavengers). At one point in their history, they were actually a lot like us. Then, so the theory goes, the Traveler came to their world. Similar stuff happened, resulting in "the Whirlwind", a cataclysm that roughly equals the Collapse. They call the Traveler "The Great Machine", and according to this theory, believe it abandoned them, and they're trying to get it back.
As for whether or not that's true...well, that's what sequels are for, am I right?
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We do know there main agenda of the fallen is to take the traveler back, but what i'm saying is they could have a side project of sorts.
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Yeah. To find a new home.