Not sure if I'd classify these as conspiracies... more like awful things that aren't widely known to the public. Look up Unit 731 and Operation Paper clip. That recently blew my mind.
TL;DR: We (The USA) hired war criminals on multiple occasions to raise our global standing in the scientific community.
Long versions:
-Unit 731: We did not prosecute Japanese scientists who experimented and tortured human subjects for the primary case of testing biological warfare and its effects on the human body. This included dropping plague-infected flea-bombs over rural China and studying the effects it had on a village's (plural, this happened many times) people. If they ever ran out of human subjects at Unit 731, Japanese secret police in occupied-China would pickup anyone from the streets.
Instead of prosecuting them, we paid for their research in exchange for their freedom from war crimes. From what I read, this was primarily due to the fact they experimented on humans, something we legally could not/cannot do, but they found the research to be invaluable... well, to be accurate, there was a determined price.
-Operation Paperclip: We hired Nazi scientists/ war criminals to lead major departments of Nasa in an effort to have an upper edge on Russia post WWII and during the Cold War. An objective point of view given was the logic, "If we didn't do it, Russia would have".