Antagonist
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Character Role Analysis
The Government
The government isn't an antagonist in the typical villain sense. It isn't trying to conquer the world, defeat the peaceful aliens, or pull any Big Brother shenanigans. At the end of the movie, we certainly aren't rooting against it; the scientists making contact with the aliens are working for the government.
Rather, the government represents fear of the unknown, an idea Roy is naturally in conflict with given his innate curiosity. Roy's aim in the film is to know what he experienced, and the government is trying to hide the facts of that experience for fear they might be dangerous.
The conflict resolves once contact with the aliens is made; Roy's goals and the government's goals become the same.