A secret CIA and NSA operation, in a Navy facility?
That suggestion lowers the credibility of this story. Those three just do not play well together.
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Why do you believe that? Take a look at a typical ship or naval installation. See all those antennas? Trace the cables all the way home and you are likely to find yourself inside some NSA complex somewhere in the world. NSA support is a perfectly legit Navy operation.
Does CIA and NSA play nice together? Maybe not supposed to. Almost certain they do.
Your post 45 is absolutely correct ... Naval Intelligence has been around a long time and it’s actually the most credible part of the story ...