I have thought about how in Indiana Jones and the Kingdom of the Crystal Skull, the Soviet Union officials are the villains, but they are shown to be acting in reaction to existing United States weaponry and technology that is threatening their country and government. RedLetterMedia does good job of explaining this in their review of the movie.
However, their main goal is to use the titular skull for mind control against Earth's population.
I actually really like the themes of the prequels. It's an example of a liberal democracy in decay that gives way to fascism, and about how liberals create tools later to be used by fascists (the Clones, for example.)
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