If aliens were the popular mythology of the 50s, JFK assassination conspiracies were definitely the popular mythology of the 60s. Is there any way it could even indirectly be tie in that could work? Say, for example, the bad guys are a consortium of rogue CIA and the Mafia. One d them could drop a line in which implies participation in JFK's murder:
"Our group has done great things for this world, Dr. Jones. Things even you wouldn't believe. We've (insert reference here). We've put kings in power. We've even...killed Presidents"
"Our group has done great things for this world, Dr. Jones. Things even you wouldn't believe. We've (insert reference here). We've put kings in power. We've even...killed Presidents"