I suppose this would be up /u/restricteddata 's alley...
Many of us know that the second atomic bombing was performed on Nagasaki as opposed to Kokura, the first choice target, due to heavy cloud cover/smoke over the latter. Even over Nagasaki, the clouds were dense, and Fat Man was only dropped when a last-minute opening appeared to reveal the target.
My question is--what was the procedure for a mission abort? As I recall, Little Boy was armed on the Enola Gay itself mid-flight due to concerns that the bomber might crash on take-off, triggering the bomb on the surface of the airbase. If a similar procedure was undertaken to prep Fat Man for use, wouldn't Bockscar have had to land back at base with a live A-bomb in the bomb bay?
I believe that B-17s and B-24s over Europe would just jettison bombs over rural areas or ocean upon an abort, but obviously this would be incredibly wasteful and hazardous to perform with a plutonium bomb...
Was there a plan for how to deal with a mission abort of this kind if the bomber had been forced to return from Nagasaki without dropping the A-bomb?
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For the Fat Man run, they would have had to jettison it in the ocean. If they had not, the added weight would have made it impossible for them to get back to a friendly airbase on the amount of fuel they had. As it was, even after dropping it, they were barely able to get to Okinawa.
As for what they would have done to the bomb itself... at that point there is nothing they would have been able to do but drop it in the ocean. There were fuzing switches on the bomb, but they could only be operated in the bomb bay, which was not pressurized. I don't think they could have deactivated it at that point. If that's the case, then it probably would have detonated over the water.
(I checked with someone, and he suggested they might have been able to drop below 10,000 feet and change out the fuzing switches. Probably quite tricky on low fuel. I suspect the explosive pressure-plugs on the front of the bomb would have probably still gone off, setting off the high explosives in a haphazard way, scuttling the contents but without a nuclear yield.)
Would it have been wasteful and hazardous? Yes indeed. A situation they all wanted to avoid. And, in fact, there is a lot of reason to think that there was no "last-minute opening" in the clouds, that instead it was aimed by radar, because if they had not dropped it on that run, they would have had to jettison it. It missed its intended target by quite a bit as a result. The decision to radar target had been pre-approved onboard (in direct contravention of official orders), but the story about the hole in the clouds opening up made this a non-issue afterwards.