Yeah he was going to expose a bunch of shady/illegal shit they and the FBI were doing. There is a conspiracy theory that he recognized the special forces as it's own distinct, largly autonomous entity because he knew his intelligence agencies were compromised. There was also the thing about him opposing a nuclear armed Israel. JFK and RFK (also assassinated shortly after JFK) were both extremely critical of the intelligence communities and basically saw them as the deep state of their time.