Starting life as the first YB-29 delivered to the United States Army Air Forces, it was sent in November 1943 to the Fisher Body Aircraft Development Section of General Motors to be converted to use Allison V-3420-17 liquid-cooled W24 (twin-V12, common crankcase) inline engines. Fisher was chosen for the modification as it was familiar with the engine, as it was to power the P-75 Eagle that they were then developing. Testing on it began in early 1944.
Further development of the engine and the aircraft was delayed by a series of changes in the planned turbosuperchargers, as the originally specified GE Type CM-2 two-stage turbosupercharger became unavailable due to demands on GE's production of its other turbosuperchargers. Other turbosuperchargers were considered, but the end result was that the first flights of the B-39 had to be made without any turbosuperchargers at all.
In addition, in early 1944, due to a sudden realization from the U.S. Army Air Force that it required a long range air superiority fighter, Fisher was directed to focus on its other major project, the P-75 Eagle. In June 1944, Fisher received a contract for 2,500 P-75s. However, in October 1944, for a variety of reasons, the P-75 was canceled.
General Motors modified B-29 to use Allison V-3420 engines
Fisher finally focused again on the B-39. The first flight of the B-39 was made on 9 December 1944 at Cleveland, Ohio. The initial flight tests of the B-39, without turbosuperchargers installed, were impressive. However, the B-39 program was by now seriously delayed, and the flawed R-3350 B-29s had already been rushed into combat in June 1944.
Despite continuing problems with the B-29s, the aircraft was functioning well enough in combat that it no longer made any sense to shift resources in the manufacturing base to a new engine for the B-29 and so the B-39 was not ordered into production.