We just rode this twice, and as much as I could tell, the alien itself is on the ceiling. There's a bunch of fog and "something" is looking out of the ceiling, but both times we rode we were on the back section of the ride vehicle, and I think the alien had "gone back" in by the time we passed under.
[Just asked my dh, and he said it's then on the RIGHT side-- they say something like "there it is again."

See how observant I must be? I never even noticed the dang thing on the side!!!]
I had bad expectations of this ride the first time we rode (in 2004) and thought my dd (then 6) would be spooked, so she and the other little girl she was riding with hid their heads through this whole section.....
I remember THAT ride I never saw the alien at all!!!
This year, dd is 8 and took pride that she was scared of nothing. She even looked right at the "ceiling version" of the alien-- I don't think she ever saw the second one, either.
It's not something that really "pops out" at you-- "Dinosaur-style" [Which, incidently, we rode at AK twice at dd8's request!!!

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