Before Major Anderson began his reconnaissance flight, Ex Comm members discussed what to do if American planes were attacked. Robert McNamara stated they should fire back. (Advance the recording to 18:45.) But no instructions to return fire were given to pilots on October 27.
Approaching San Julian Airfield, outside Havana, Major Anderson was shot down by Soviet surface-to-air missiles. He would not have known the area he previously surveyed was now a fully operational SAM site with operators about to grant Castro’s wish.
Alekseev sent another telegram (scroll down about 25%) to Moscow, reporting the hit:
Castro told how a U-2 airplane had been shot down from an altitude of 21 kilometers, and that the Cuban military powers
had collected its fragments and the corpse of its pilot.
JFK learned of the shooting shortly after he had agreed to a strategy that could end the crisis. It was a strategy, implemented by his brother Bobby, known only to a few people. The secret was kept for nearly 30 years.