2. The Defense Intelligence Agency and the US Navy provided the first clues to Soviet activity
With new information from daily U-2 flights no longer available, analysts at the Defense Intelligence Agency (DIA) began a closer study of the photographic evidence available in September. One of the first clues that the Soviets were installing, or intended to install, offensive nuclear missiles was discovered by DIA when they noticed that the pattern of the launch sites for their surface-to-air missiles (SAM) was similar to those in the Soviet Union, installed to protect intercontinental ballistic missile (ICBM) sites. The presence of Soviet “advisors” on the island was already well known. At the same time US Navy reconnaissance photos of Soviet ships revealed the presence of shapes on their decks which resembled the fuselage of nuclear strike bombers.
Armed with the evidence of weapons with the potential of delivering nuclear weapons on targets in the United States being installed in Cuba, DIA and the Office of Naval Intelligence began pressing their civilian bosses in the Kennedy Administration to restart the U-2 surveillance flights over Cuba. The Air Force joined in the lobbying effort, arguing that responsibility for the resumption of U-2 flights should be theirs, rather than the CIA, who had operated the flights (and analyzed the data) before they were suspended. On October 9 the resumption of U-2 flights, under Air Force supervision, was authorized. For several days poor weather prevented any flights, the cloud cover over the island meant that the flight could not take any useful photos. On October 14, the weather cleared sufficiently for flights to resume.