Well, OP, your question is kind of vauge - it implies you don't believe the official story; however, The documents are declassified. You can read them yourself. In fact lots of documents on the project have been.

The long and short of it is the CIA was experimenting with behavior modification. The project began in the 1950's and concluded in the 1970's. The project itself was broad and encompassed a lot of things; however, it's main focus was interrogation. They wanted to know how to weaken an opponents / prisoners mental defenses or find a way to force them to tell the truth.

Sometimes those who were involved in the project had no idea they were involved. Some of the experiments were run by civilian hospitals and universities. That's pretty much the quick version of it.

I'd advise reading the documents that have been declassified - I linked them above. That will give you a first hand account.