It seems to me very likely that JFK ordered someone to assassinate Fidel Castro, for three reasons: first, if such an assassination could have been accomplished, it would have been a good thing for the United States (or, at least, the United States would have expected it to be a good thing); second, the decision to assassinate or not assassinate Fidel Castro would likely have been left to the president; and third, the testimony of several individuals circumstantially indicates that JFK did in fact attempt to have Castro assassinated.
Ultimately, my reasoning rests, interestingly enough, on the actions and testimony of Helms. Helms has said that he never received a “direct order” from JFK; however, I have several reasons for believing that that is a lie, that he received indirect but clear orders, or that JFK ordered Robert Kennedy to ensure the assassination.

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First and foremost, a considerable amount of effort went in to advancing the position that JFK did not know about the assassination attempts that were underway when he took office. However, in light of the evidence, this is not credible. Testimony was given that he did know about the bay of pigs invasion, as president-elect, but that he was not informed of project MONGOOSE. Justifications for this discrepancy were relatively implausible — if JFK needed to know about the Bay of Pigs invasion as president-elect, surely he also needed to know about the attempted assassination of Castro. This seems even more clearly true when we consider that the National Security Advisor knew about the plans, and would likely have wanted to discuss them with Kennedy.

This alternative understanding is lent credence by the witness testimony. Someone had probably, according to Smathers, discussed assassination with JFK (Church 124). That Smathers’ testimony suggests that JFK knew about the assassination plans should not be surprising; that he did not believe JFK to have been the authority behind the plans’ continuance is more surprising. The only reason, in my judgment, that one would want to conceal that JFK knew about the assassination plans is to forestall investigation into whether he ordered those plans, either directly or indirectly.

My belief that there was a direct order from the president is further supported by the actual operational rules that were in effect. It was impermissible to order assassination without direct orders (147-148). I don’t mean to suggest that the CIA never did anything against the rules, but I do think that this is indicative of a general pressure such that Helms in particular would have had to be convinced that someone with the authority to give such an order at least wanted the assassinations to continue. Moreover, the framing of Helms’ “absence of direct order” doesn’t preclude indirect orders, which is what I believe is most likely. It seems to me that the most likely mechanism is that JFK ordered the assassination attempts through his brother, Robert Kennedy, and that Robert Kennedy was the one who bore the burden of directly ordering others to continue progress with project MONGOOSE (150).

To be frank, the possibility that JFK did not know about the assassination attempts is ludicrous. Accepting that he did know, either everyone was careful not to bring up the assassinations in a context in which he would have to express his opinions on them (and an expression of support for them would have the force of an order, just stated differently) — and again, this does not appear to be the case — or he did, in fact, wind up affirming his support for the assassination of Castro. I believe that this is more likely.

    References
  • “Church Committee Report, Alleged Assassination Plots Involving Foreign Leaders.” 1975. Church Committee.