To me it's most rational to assume that governments/military do do shocking, immoral, counter-intuitive things, because their game and stakes are so high, and just accept it as the natural, rational way that they would behave. It seems a lot more likely than them not doing it. If you accept that, then all the excitement and paranoia of conspiracy theories goes away.
What you also need to include is the puppet master of corporate interest. Just follow the money, no act is so despicable it does not have a price worth stealing.