On October 23, 1962, a U.S. Navy commander named William B. Ecker took off from Key West at midday in an RF-8 Crusader jet equipped with five reconnaissance cameras. Accompanied by a wingman, Lt. Bruce Wilhelmy, he headed toward a mountainous region of western Cuba where Soviet troops were building a facility for medium-range missiles aimed directly at the United States. A U-2 spy plane, flying as high as 70,000 feet, had already taken grainy photographs that enabled experts to find the telltale presence of Soviet missiles on the island. But if President John F. Kennedy was going to make the case that the weapons were a menace to the entire world, he would need better pictures.

Swooping over the target at a mere 1,000 feet, Ecker turned on his cameras, which shot roughly four frames a second, or one frame for every 70 yards he traveled. Banking away from the site, the pilots returned to Florida, landing at the naval air station in Jacksonville. The film was flown to Andrews Air Force Base outside Washington, D.C. and driven by armed CIA couriers to the National Photographic Interpretation Center, a secret facility occupying an upper floor of a Ford dealership in a derelict block at Fifth and K streets in Northwest Washington. Half a dozen analysts pored over some 3,000 feet of newly developed film overnight.

At 10 o’clock the following morning, CIA analyst Art Lundahl showed Kennedy stunningly detailed photographs that would make it crystal clear that Soviet leader Nikita Khrushchev had broken his promise not to deploy offensive weapons in Cuba. As the Cuban missile crisis reached its peak over the next few days, low-flying Navy and Air Force pilots conducted more than 100 missions over the island in Operation Blue Moon. While Kennedy and Khrushchev engaged in a war of nerves that brought the world the closest it has ever come to a nuclear exchange, the president knew little about his counterpart’s intentions—messages between Moscow and Washington could take half a day to deliver. The Blue Moon pictures provided the most timely and authoritative intelligence on Soviet military capabilities in Cuba, during and immediately after the crisis. They showed that the missiles were not yet ready to fire, making Kennedy confident that he still had time to negotiate with Khrushchev.

In the 50 years since the standoff, the U.S. government has published only a handful of low-altitude photographs of Soviet missile sites—a small fraction of the period’s total intelligence haul.

When I was researching my 2008 book on the crisis, One Minute to Midnight, I came across stacks of declassified American intelligence reports based on the Blue Moon photographs. I assumed that the raw footage was locked away in the vaults of the CIA until I received a tip from a retired photo interpreter named Dino Brugioni. A member of the team that prepared the photo boards for Kennedy, Brugioni told me that thousands of cans of negatives had been transferred to the National Archives, making them available for public inspection—at least in theory.

That tip launched me on a chase that led to a National Archives refrigerated storage room in Lenexa, Kansas, nicknamed “the Ice Cube,” the final resting place for hundreds of thousands of cans of overhead imagery taken during and after the missile crisis. To my surprise, no one had ever requested the Blue Moon material. Researchers are not permitted at the Ice Cube, but they may order ten cans of film at a time, which are then air-freighted to the National Archives facility in College Park, Maryland. There is just one catch: The cans are numbered in a seemingly haphazard fashion, and the CIA finding aid for the materials is still classified. Without it, requesting cans of Blue Moon film seemed like a hopelessly long shot.

I desperately needed the help of the researcher’s old friend, luck, and I got it when I stumbled across the identification number of one of the missile-crisis cans in a document I found in the Archives. Beginning with that number, I ordered random samples of cans until I had identified the shelves where the Blue Moon material was generally located. In all, I examined nearly 200 cans of film containing several thousand photographs.

The film brings home the dangers and difficulties the pilots faced. Working long before the invention of automated GPS systems, they navigated primarily with maps and compasses and used landmarks like bridges and railroads to find their targets. Flying over the treetops at 550 miles per hour, they had to operate a battery of cumbersome cameras while keeping an eye out for construction sites, military vehicles or other “suspicious activity.” To take useful pictures, they had to keep their platforms steady and level for the all-important few seconds they were over the target. The risk of mechanical failure or getting shot down was more or less continuous from the moment they entered enemy territory.

Each reel seats the viewer in the cockpit: Early frames typically show the ground crews at the naval air station on Key West checking out the cameras and planes. Surf splashes up against the Crusaders’ fuselages as they fly low across the Straits of Florida and cross the beaches of northern Cuba before heading over the island’s mountains. Plazas and baseball diamonds suddenly give way to missile sites and military airfields. In one series of images, the landscape goes suddenly haywire: The pilot has yanked his joystick to avoid anti-aircraft fire. As I reeled through the 6-by-6-inch negatives on a light table similar to the one the CIA’s photo interpreters used, I found myself holding my breath until the pilot escaped back over the mountains to the open sea.

In addition to bringing the viewer back into the moment, the photographs offer insights into the gaps in American intelligence-gathering—instances in which the CIA misinterpreted or simply ignored information it collected. One example is the photograph of a munitions bunker near the town of Managua, south of Havana.