WASHINGTON  Is the Central Intelligence Agency covering up some dark secret about the assassination of John F. Kennedy?

Probably not. But you would not know it from the C.I.A.’s behavior.

For six years, the agency has fought in federal court to keep secret hundreds of documents from 1963, when an anti-Castro Cuban group it paid clashed publicly with the soon-to-be assassin, Lee Harvey Oswald. The C.I.A. says it is only protecting legitimate secrets. But because of the agency’s history of stonewalling assassination inquiries, even researchers with no use for conspiracy thinking question its stance.

The files in question, some released under direction of the court and hundreds more that are still secret, involve the curious career of George E. Joannides, the case officer who oversaw the dissident Cubans in 1963. In 1978, the agency made Mr. Joannides the liaison to the House Select Committee on Assassinations  but never told the committee of his earlier role.

That concealment has fueled suspicion that Mr. Joannides’s real assignment was to limit what the House committee could learn about C.I.A. activities. The agency’s deception was first reported in 2001 by Jefferson Morley, who has doggedly pursued the files ever since, represented by James H. Lesar, a Washington lawyer specializing in Freedom of Information Act lawsuits.