After WW2, the US started mothballing and selling off every warplane in inventory as they adjusted to peace time fiscal reality. Certain government agencies weren't about to write off the longest range plane the US had ever built, the B-29, and with the advance of Communism the CIA set about checking it's advance around the world. And for all of you who don't buy into conspiricy theories, the B-29's were painted black.
The B-29 allowed the US Air Force to pound the Japanese back to the stone age, bringing an end to WW2. The plane was not without it's problems, as it pushed the limits of propeller driven technology along with high altitude flying. The big 4 row radial engines would easily overheat just waiting to take off. The remote controlled guns gave trouble, and just keeping the plane pressurized was scary.... now and then a plexiglass canopy would blow off, leading to serious decompression. When the CIA entered the picture after WW2, they had a different plan for the B-29. The operational requirements were for long range planes that could carry a good load, but usually delivered at 500 feet at low speed. This was to allow dropping agents out a "Joe hole" in the bottom of the plane, and to reel in other agents to be plucked from the ground. The B-29 was ill suited for this kind of stuff, and skirted stalling every time it flew that slow. And at 500 feet, there is no recovery.
When the planes were modified for this clandestine activity, all the guns except for the tail gun were removed, leaving the plane defenseless, but nevertheless no crews bowed out of a mission. The bomb bays were used for dropping leaflets and supplies to clandestine anti-communist units. The newly formed CIA and the Air Force collaborated at the top levels and formed three wings with thousands of personnel, most of which were in the dark because of the need to know philosophy. These wings were known as Air Resupply and Communications Wings or ARC. They operated out of three main places around the world, England, Libya and the Philippines.
There were planes that didn't come back, the most famous being the Stardust Four Zero mission in 1953, in which a lone B-29 flying over North Korea within spitting distance of China was easily taken down by a flight of Russian Mig 15's, on loan to China at the time. The captured fliers didn't get home till 1955. ARC was stood down by January of 1954.
Links:
War Tales Florida man flying Clandestine missions
Aircraft shot down during the Cold War