I'm pretty certain that the entire pyramid will not fly away at the end. A couple of months ago, I posted my could-kinda-sorta-be plot summary where I tried to tie together all known information. If anyone remembers that, which I doubt you do, I made mention that the Aztecs and Mayans built their temples around already existing previous temples - with each new incarnation being larger and taller than the last. They didn't demolish them and start over from ground zero. Lucas has said that they try to tie in historical fact in everything they do Indy related, and keeping all this in mind, what if the Mayans simply built their temple around and on top of an already existing spaceship? The most sacred innards of the temple would actually be the interior of this ship.
OMG dood, that would suck!!!11 Spaceshipz doo not belung in Indy Jonez!! LOL!!1 You r an idot!
Well. You know. With a few sacks of acme dust and vines draping everything, I bet you almost wouldn't notice. Maybe the architecture of the Mayans is taken from the decoration of the spaceship because they regarded it as a vehicle of the gods. In this way, everything would retain that Meso-American, old world Indy look. As an added bonus, it would actually make sense this time when the crew has to exit the temple in a hurry because everything is tumbling in around them. Outside, they see the ship crowning out of the temple and sloughing off tons of quarried limestone rocks.
And these Close Encounters aliens?
Like it has already been mentioned, if they appear, it will almost certainly be in the same fashion as that R2D2 and C3PO "cameo" in Raiders.