Due to the Cuban Missile Crisis, JFK was read into the existence of aliens who would intervene during a MAD event. Apollo was not because it's "hahhd" or to inefficiently develop missile tech, but to reach out to aliens on their moon base as show of peace/strength. Upon contact, JFK was going to go public, against conventional wisdom that it would cause mass hysteria and a breakdown of society, a cost deemed worthy of assassinating a sitting President. He'd told Marilyn Monroe and Bobby before death. They were silenced.
