Aliens (from what I understood of the plot) deeply wanted the 13th Crystal Skull returned back to their circle of skeletons, so they could re-animate, meld/merge, and get the hell out of Dodge this planet.

This is clear because they told Indiana Jones (and presumably, Oxley before him) to return the skull.

Yet, they also caused a warlike, hostile tribe of natives, to be preventing anyone who would return the skull, from getting it into the pyramid - first, Oxley couldn't get by them and had to return the skull to the original place (this is important, because Oxley had the skull with him the first time around, and couldn't get by them). Then, Indiana Jones and Transformer Jr. barely escaped with their lives even AFTER showing the natives the skull (which was presumably how they were supposed to tell friend from foe - but didn't help Oxley at all).

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    Wait.... you understood part of the plot of that movie? I didn't even realize there was a plot. – BBlake Nov 4 '15 at 13:54
  • @BBlake - it's like an ancient relic. You must be really good to find it – DVK-on-Ahch-To Nov 4 '15 at 13:56

Why did the aliens get natives to prevent the return of the Crystal Skull by threatening its carriers?

They didn't.

At this point, the "inter-dimensional beings" had been dormant for several millennia. The natives simply lived at the temple and likely tried to kill anyone they deemed a threat, as fictional natives are wont to do.

As to why they stopped trying to kill them when they saw the skull? It appears most living creatures try to avoid it, as seen with the ants, who had nothing to do with it or the aliens.

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