I couldn't even begin to speculate how the HL2 arc will be resolved, but I could actually see an ending to Ep. 3 like that.
Picture this; you're
almost close to some kind of enlightenment on what's actually going on in HL2. Some character is
just about to say something that'll put all the pieces together, finally. Then
something happens. Then suddenly you're on the monorail. The end of Ep3 plays out like the start of HL1.
"Was it all a dream? What the fuck is this?" you will say. Then
something really weird happens. Just for a split moment. Maybe all the humans you see around Black Mesa suddenly appear to be Vortigons,
just for a flicker. Maybe the announcer of the train says something really weird and random (I've got that whole speech committed to memory). Just enough to make you question it. Then fade to black...
I wouldn't put it past Valve to pull some kind of shenanigan like that.