Nosenko was locked in a small room and interrogated for more than three years, while a battle raged within the CIA over his bona fides.
Because this issue was unresolved during the Warren Commission's tenure, the Commission received reports about him but did not use his information in its publications.
A prominent Warren Commissioner was former CIA Director Allen Dulles, who Kennedy had let go after the Bay of Pigs fiasco.
Dulles maintained some contact with the Agency during the Commission's tenure, including coaching it on what questions the Commission might ask; one internal memo summarizing such a contact included this: "I agreed with him [Dulles] that a carefully phrased denial of the charges of involvement with Oswald seemed most appropriate." The ill-fated investigation of New Orleans District Attorney Jim Garrison into the Kennedy assassination was not running for long before it started to pull CIA assets into its sights.
This changed with the ill-fated Bay of Pigs invasion of Cuba, inherited from the Eisenhower administration.
Kennedy accepted responsibility publicly, but privately blamed the CIA and obtained the resignation of longtime Director Allen Dulles and others.
He also implemented NSAM 55, transferring control of paramilitary operations to the Defense Dept.
For their part, many CIA officers and Cuban exiles blamed Kennedy for failing to support the operation, in particular canceling a planned second set of airstrikes.
Senator Richard Russell, when informed of the situation, was among those who advocated immediate military action to remove the missiles, telling Kennedy: "It seems to me that we are at a crossroads. And I think that we should assemble as speedily as possible an adequate force and clean out that situation." CIA officer William Harvey sent commando teams into Cuba during the crisis, which earned him the emnity of the Kennedys and eventual exile in Rome.
During 1963, plans for the overthrow of Castro continued, while the Kennedy administration simultaneously began pursuing a "second track" of accomodation.