"Pentagon officials suggest . . . draft document . . . could be . . . potentially . . ."
↑ Note the key words. This 'report' is highly speculative at best, and pure disinformation/distraction at worst.
While you are searching outer space for a 'mother ship', the pentagon is doing something on the sly elsewhere.
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The mere fact that science may not yet adequately explain an object, event, or experience does not mean the immediate explanation should automatically default to a conspiratorial, extraterrestrial, paranormal, or supernatural cause.