Reverse Engineering of UFO Technology

I've been reading up in UFOs lately because I'm writing a novel on the side which includes UFOs. To the extent that that is actually something that's happened, there's been craft that have crashed or been retrieved and then the US government's been trying to reverse engineer that technology. How plausible is it that such a secret could be kept hidden for so long? And how would you nest a project like that within the Department of Defense? Well, interesting questions. They had Area 51 and they had the, what was it called? Were they built the U2s and the? Oh, yeah.