Sure there are. For example, the existance of F-117 stealth fighter remained secret for more than 10 years after it became operational! That's quite an achievement. But the crucial difference between this kind of secret and "hiding the evidence of ET's" is that everyone involved in the former knows there is a good reason for the secret and moreover, should they spill it, American public opinion would be against them. A secret which involves hiding something as important as existance of ET's for no good reason is a different story -- and covering it up through murder is even more of a different story. In fact, if anyone involved went to CNN and told the whole story, his life would be utterly safe. Nothing would collaborate the story more than him suddenly dying -- and if the killers were caught (yes, plenty of detectives, policemen, and military investigators would remain faithful to their duty, not to mention reporters), the backlash would destroy any Administration.

That's why I always laughed at the theory that Flight TWA 800 was shot down by a US Navy missile. On any ship with more than 100 crewmen you'll find at least one (usually more) sailor who hates the Navy and would love nothing more than stick it to the Navy and to his captain. If the airliner were actually shot down by a missile, or even worse, the crew were ordered not to talk about it, this sailor would be on the phone to CNN the very next shore leave. And there is nothing Navy could do to him after the fact. In view of American public (and in truth) he'd be a hero. The fact that not one sailor came forward with the story is the best proof to me that it never happened.

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Fiction has to be plausible. Reality is under no such constraint.