Bill Cooper describes seeing flying saucers fly up and down into the water next to his submarine, when he was a Navy officer in 1960s. He describes multiple crew members seeing them on multiple occasions and that there was "a lot of traffic", lots of photographing of them, etc.
The explanation that fits the best is that those were just NWO (Bush/Hitler) aircrafts, and that the US Navy (under NWO control by then) were testing the loyalty of their crew. That the "Breakaway civilization" is just Bush/Hitler's New World Order, controlling much of global politics and having access to "advanced" technology developed over the past 70 years, kept secret because why not.
The "Breakaway civilization" is our civilization, the parts of it that have obviously subverted control of most other parts of it. Not some "other" that is completely hidden out of sight.
The personal that kept their secrecy likely got a raise, Bill Cooper, one of few who did not, was simply killed. Mystery solved. Military organizations kill people all the time, for simple practical reasons. Had he been a little less outspoken it would have been unnecessary to kill him, but since he was excellent at blowing the whistle on the NWO they took him out. Had he conformed instead they would have rewarded him and given him a raise and a promotion.