Nagasaki Wasn't Supposed to Be the Second Atomic Bomb Target

In early August 1945, Nagasaki, Japan, became the unintended target of America’s second atomic bomb. Among the casualties: Japan’s largest and oldest Catholic enclave.

In the predawn hours of August 9, 1945, at an American Army Air Force base on the Pacific island of Tinian, crews prepared a B-29 bomber named Bockscar for a mission. Loaded aboard was a rotund plutonium-cored atomic bomb, dubbed “Fat Man” by its Manhattan Project designers. The bomb packed nearly 25 percent more power than the uranium-cored “Little Boy” that had destroyed Hiroshima three days earlier.

Bockscar’s pilot, Major Charles Sweeney, had received orders to drop Fat Man on Kokura, an Imperial Japanese Army arsenal on the northern coast of Kyushu, the southernmost of Japan’s four main islands. The drop was contingent on whether Sweeney’s bombardier, Captain Kermit Beahan, could visually identify the aiming point. If not, Bockscar was to proceed to the day’s secondary target, Nagasaki, a harbor town on the western coast of Kyushu and one of Japan’s oldest foreign trading ports.

While Bockscar was taxiing for takeoff one time zone away and some 1,500 miles to the southeast, 22-year-old novice Sister Itonaga Yoshi was beginning her day on the campus of Junshin (“Immaculate Heart”) Jogakkō, a Catholic girls junior high and high school in the Urakami valley, an industrial and suburban district in northern Nagasaki. The valley was home to two Mitsubishi naval munitions plants—and also to the largest and oldest Catholic community in Japan, established in the late 16th century by Portuguese Jesuits. Sister Yoshi, a direct descendant of the first generation of Japanese converts, was proud that her Catholic ancestors had preserved their faith despite having endured centuries of persecution by Japan’s ruling Shogunate.

Following their daily Matins devotions, Sister Yoshi and the other Junshin novices began preparing breakfast for senior faculty and 600-odd students. More than 500 of them were scheduled for another day of toil as war-mobilized labor in the Mitsubishi torpedo plant across the street. After the morning meal, the Junshin order’s Mother Superior and school principal, Sister Magdalene Yasu Esumi, told the school faculty about Hiroshima’s destruction on August 6. As a precaution, she ordered first-year local students to return home to their families, and the first-year boarders to evacuate with faculty chaperones to the mountains north of the city.

Older girls, still part of Japan’s war effort, were required to report for their munitions work. Sister Yoshi escorted a group of about 30 Junshin girls to a metal foundry in Togitsu, roughly three miles north.

In an alternate destiny, Nagasaki would have emerged from World War II relatively unscathed—appreciated more for its postcard-pretty harbor views, exotic Christian heritage, quirky Victorian architecture (relics of its 19th-century Eurocentric heyday)—and its role as the setting for Giacomo Puccini’s beloved opera “Madama Butterfly.”

Kokura—not Nagasaki—would have gone down in history as Hiroshima’s sister city in atomic devastation.

But that was not to be. Poor visibility over Kokura and a cascade of mishaps—a faulty fuel system, a missed rendezvous with the other strike force bombers and some questionable calls by Sweeney—put Nagasaki in the crosshairs instead.

At approximately 10:50 a.m. local time—eight hours into the mission and two hours after Fat Man was supposed to have exploded over Kokura—Bockscar, now low on fuel, began its bomb run toward Nagasaki’s densely populated central business district. Haze again obscured the aiming point. The navigator reported only enough fuel for one pass over Nagasaki—barely enough to make it to Okinawa, the nearest friendly airbase—that is, if they weren’t carrying the dead weight of a five-ton bomb.

With Beahan still coming up empty and the seconds ticking down toward a Go/No Go call for a drop, Sweeney had to choose: drop the bomb by radar against orders, or jettison it into the sea and risk ditching the plane in the Pacific. Then came the break in the clouds.

The flight log that might clarify what happened has been missing since the end of the war. What can be confirmed is that, at 11:02 a.m. local time, Fat Man detonated at an altitude of 1,650 feet above the Urakami valley—just over two miles north of its original target.

Captain Beahan’s deviation from mission parameters—and the vagaries of local topography—saved Nagasaki’s central business district from complete destruction. But it eviscerated the city’s Catholic community. By year’s end, 40 percent of its 20,000 members and 65,000 other Nagasakians were dead—from some combination of the bomb’s heat, blast force and radiation.

Within a roughly two-kilometer radius of Ground Zero, anyone caught outdoors at the moment of detonation had been essentially blowtorched alive by the bomb’s fireball—the thermal rays of which baked any exposed surface for up to eight seconds at temperatures twice the melting point of steel. According to the International Campaign to Abolish Nuclear Weapons, ground temperatures reached 4,000 degrees Celsius. In a grim sense, they were the lucky ones: The bomb’s initial shock wave ended their lives ended almost immediately, sparing them the prolonged agony so many others would endure.

Far more Nagasaki victims took longer to die—either from burns and blast injuries, or trapped under the burning debris of the thousands of collapsed wooden houses, factories, schools and churches. Unluckiest of all were the acute radiation syndrome victims—perhaps a fifth of the city’s total fatalities—who succumbed after prolonged, agonizing deaths, their internal organs failing one by one as their bodies decomposed from the inside out.

Sister Yoshi, far enough away to escape serious harm, made her way back to the ruined campus through a hellscape where thousands of scorched and maimed victims were fleeing the burning city. She joined surviving nuns to search for Junshin’s students under the toppled machinery and twisted girders of the collapsed and still-burning Mitsubishi plant. The dead—who were in the majority—were cremated on Junshin’s athletic grounds.

Over the following days and weeks, distraught family members searching for missing daughters or sisters arrived at Junshin, only to be handed wooden boxes containing their loved ones’ ashes. The remains of girls that went unclaimed—likely because their families also died—lie today under the base of a white marble statue of the Virgin Mary, a gift to the school from American Catholics. Since 1949, the statue has stood vigil over the main gate of the rebuilt Junshin campus. On its plinth, a bronze plaque bears an epitaph:

In the flames of burnt sacrifice

The girls of white lilies

Rose up to the bosom of the Lord,

Singing the glories of peace.

Sister Yoshi died in 2022, just shy of 100 years old. She was the last order member who had been wearing the habit of a Junshin sister when Fat Man rained hell over the Urakami valley.