Just scanning the web, I found a site which gives you a good take on his view of E.T.s -- www.williamcooper.com/area51.htm.
His book, "Behold a Pale Horse," is an interesting read, and I think it's a shame he's dead.
Allusions seemed to be made that advanced electronic warfare and studies in mental phenomenon had led to a state of art wherein dreams could be induced, voices planted in one's thoughts, other ideas or emotions induced, etc.
Seems like Cooper advanced the notion that the alien abduction reports were actually real military encounters with the encounter cloaked by a false image being imparted on the unwitting observer or passer-by. Sort of a tangent to the Men-in-Black flashing ball point pen resetting a person's memory only with reidentifying any person during the encounter as an alien form.
My impression of his death is analagous to a visitor in Crete witnessing a conflict between a Turk and a Greek patriot. One might not know who started what, and understand arguments defending both points of view rigorously, but at least one could glean a very real conflict existed.