Robert A Heinlein

First came the news that a flying saucer had landed in Iowa. Then came the announcement that the whole thing was a hoax. End of story. Case closed.

Except that two agents of the most secret intelligence agency in the US government were on the scene and disappeared without reporting in, as did four other agents who were sent in. As a result, the head of the agency and his two top agents went in, and they managed to get out with their discovery:

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When the U.S. is occupied by an invading army, six individuals secretly work on a weapon to help restore freedom to the world.