Bockscar had been flown by Sweeney and crew C-15 in three test drop rehearsals of inert "Fat Man" assemblies in the eight days leading up to the second mission, including the final rehearsal the day before. Rather than move the instrumentation from The Great Artiste to Bockscar, a complex and time-consuming process, the crews of The Great Artiste and Bockscar switched planes. The result was that the bomb was dropped by Bockscar, flown by the crew C-15 of The Great Artiste.
There was confusion over the name of the plane because an initial eyewitness account by reporter William L. Laurence of the New York Times said that the second bomb had been dropped from The Great Artiste. Laurence, who accompanied the mission as part of Bock's crew, had interviewed Sweeney and his crew in depth and was aware that they referred to their airplane as The Great Artiste. Except for Enola Gay, none of the 393rd's B-29s had yet had names painted on the noses, and unaware of the switch in aircraft, Laurence assumed victor 77 was The Great Artiste.
Kokura was the primary target, but when Bockscar arrived at its rendezvous point off the coast of Japan the third aircraft of its flight (the photo ship Big Stink) was not present. After fruitlessly waiting 40 minutes, Sweeney and Bock proceeded to Kokura but found it obscured by clouds. Sweeney had orders to drop the atomic bomb visually if possible, and after three unsuccessful passes over Kokura, conferred with weaponeer Commander Frederick Ashworth (USN). They agreed to strike the secondary target, Nagasaki. A combination of factors including confusion about a malfunctioning transfer pump made fuel consumption a critical factor. Ashworth did not want to be forced to dump the bomb into the sea and decided to make a radar bombing run if necessary. However, enough of an opening appeared in the cloud cover to allow Bombardier Kermit Beahan to confirm Nagasaki and the bomb was dropped, with ground zero being about 3/4 mile from the planned aiming point. This combined with Nagasaki's position on the foothills (as opposed to Hiroshima's mostly flat terrain) resulted in lower overall casualties than in Hiroshima, with much of the blast confined in the Urakami Valley.
Because of the delays in the mission, the B-29 did not have sufficient fuel to reach the emergency landing field at Iwo Jima, so Major Sweeney flew the aircraft to Okinawa, where, despite being unable to make contact with the control tower, he made a safe landing with virtually empty fuel tanks.
Bockscar, B-29-36-MO 44-27297, victor number 77, was assigned to the 393rd Bomb Squadron of the 509th Composite Group. One of 15 Silverplate B-29s used by the 509th on Tinian, Bockscar was built at the Glenn L. Martin Aircraft Plant at Omaha, Nebraska at what is now Offutt Air Force Base, as a Block 35 aircraft. It was one of 10 modified as a Silverplate and re-designated "Block 36". Delivered on 19 March 1945, to the USAAF, it was assigned to Capt. Frederick C. Bock and crew C-13 and flown to Wendover Army Air Field, Utah.
It left Wendover on 11 June 1945 for Tinian and arrived 16 June. It was originally given the victor number 7 but on 1 August was given the triangle N tail markings of the 444th Bomb Group as a security measure and had its victor changed to 77 to avoid misidentification with an actual 444th aircraft.
Bockscar was also used in 13 training and practice missions from Tinian, and three combat missions in which it dropped pumpkin bombs on industrial targets in Japan. Bock's crew bombed Niihama and Musashino, and 1st Lt. Don Albury and crew C-15 bombed Toyama.
It returned to the United States in November 1945 and served with the 509th at Roswell Army Air Field, New Mexico. It was nominally assigned to the Operation Crossroads task force but there are no records indicating that it deployed for the tests. In August 1946 it was assigned to the 4105th Base Unit at Davis-Monthan Army Air Field, Arizona, for storage.
At Davis-Monthan it was placed on display as the aircraft that bombed Nagasaki, but in the markings of The Great Artiste. In September 1946 title was passed to the Air Force Museum (now the National Museum of the United States Air Force) at Wright-Patterson Air Force Base, Ohio, but it was not moved there until 26 September 1961, where its original markings were restored.
Bockscar is now on permanent display at the National Museum of the United States Air Force, Dayton, Ohio. This display includes a replica of the "Fat Man" bomb and signage that states that it was "The aircraft that ended WWII". This is in contrast to the display of Enola Gay at the Smithsonian's Steven F. Udvar-Hazy Center, where little mention is made of that aircraft's role in WWII.
In 2005, a short documentary was made about Charles Sweeney's recollections of the Nagasaki mission aboard Bockscar, including details of the mission preparation, titled "Nagasaki: The Commander's Voice."
Crew C-15 (normally assigned to The Great Artiste):
Also on board were the following additional mission personnel: