... The first demand [the Kennedy administration made after the discovery of nuclear missiles in Cuba] was that the Soviets begin removing the missiles within 48 hours, or the United States would attack them. This part was soon publicly known. The second demand, which long remained secret, was that firing on American reconnaissance planes must end immediately. According to Daniel Ellsberg’s notes from the higher-than-top-secret 1964 study he conducted of the crisis for the Department of Defense, the attorney general declared, “If one more plane was shot at, we wouldn’t just attack the site that had fired at it; we would take out all the SAMs and anti-aircraft and probably all the missiles. And that would almost surely be followed by an invasion.”

As Ellsberg recounts in his penetrating new memoir, The Doomsday Machine: Confessions of a Nuclear War Planner, American officials assumed that Khrushchev had authorized the anti-air firing on U.S. planes. In fact, however, Cuban personnel were conducting operations under the direction of Fidel Castro. On Saturday morning, the 27th, Castro feared an imminent invasion and ordered his anti-aircraft personnel to fire on American planes. Some Soviet operators were carried away by the example of their Cuban comrades and ignored orders not to fire without the express authorization of the Soviet general in charge in Cuba. This turned out to be the case with the local SAM commander, who ordered the firing that downed the U-2 plane on Saturday, as Ellsberg recounts, drawing on much later scholarly research.

In other words, the Kennedy brothers had issued an ultimatum that other American officials (and the public) did not know about, and which they could not confirm Khrushchev received. The Kennedys did not consider that Castro and his forces were acting independently, and therefore that their immediate ultimatum would not reach this key actor, whether or not he would heed it. Signals were being sent assuming they would be received and acted upon by the right actors, but American leaders did not know that they did not know who the right actors were, or that the messages were being received as intended.

These were not the most dangerous unknown unknowns. For, until 1992, at a conference in Cuba of American, Soviet and Cuban veterans of the crisis, no Americans knew that the Soviets had deployed more than 100 “tactical” nuclear weapons in Cuba. These smaller, battlefield-oriented nuclear weapons were to defend against an expected Marine invasion by the United States. Prior to October 22, local Soviet officers were pre-authorized to use them against an American invasion force. The Kennedy brothers and all their advisers had mistakenly thought that the only nuclear-related forces on Cuba were medium- and intermediate-range missiles; intelligence assets were searching for those missiles’ corresponding nuclear warheads, but had not been able to locate them. The deployment of tactical nuclear weapons was unknown, and the delegation to use them utterly unimaginable to American intelligence analysts and leaders.

Had another American plane been hit, the United States probably would have responded first by bombing missile installations. ...