When the little boy and fat man were dropped OTL, thankfully the Japanese air force had largely ceased to exist. But what if you needed to drop one on somewhere contested, say Moscow? How would you ensure the bomb got there?
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My $.02 worth.. (and I expect I am missing a lot points..)
Get intelligence on stuff such as radio frequencies used by the defenses for Ground Control Interception (ie. sending instructions from the ground to interceptor air craft.)
Get intelligence on radar systems (ie. Early Warning, Ground controlled intercept, Gun laying etc..) used by the defenses.
Get intelligence on any proximity fuses the defenses may use.
Gather WW2 veterans with the needed skills and the necessary equipment to deal with (ie. jam, spoof or ?) the likely threats based on the intelligence collected.
Figure out what existing navigation aids can be used to find the target at night and find veteran B29 air crew with some experience in using such aids (there are probably two or more parts to this problem , finding the target area, and dropping the bomb(s) at the desired point which will likely be done at night and thru cloud cover.)
See if any assets on the ground near the target area could be expected to provide real time weather info to the bombers via radio to help with bomb aiming (ie wind speed and direction ?)
Probably look into fusing methods for the nuclear weapons that can't be jammed or spoofed and assume any methods used during the missions over Japan were compromised.
Discretely practice in an out of the way area.
Maybe fly a few non nuclear missions into the target nations airspace to collect and or confirm some of the intelligence information.
Pick a dark (ie. no moon and preferably lots of clouds at various altitudes if possible) night for the nuclear mission(s) (so that non radar equipped air craft will struggle to carry out an interception, search lights from the ground won't help much if at all etc..)
If possible fly several aircraft via different routes but at more or less the same time to maximize the chances of getting at least one of them over the target and having at least one bomb detonate over the desired ground zero.
IMHO so long as the defenses didn't have sams or post WW2 radar equipped Jet powered interceptors there would be a reasonable likelihood of getting an aircraft to the bomb away point, depending on how much information was known about the sams or Jet Powered radar equipped interceptors the mission might also still work but success would be less likely in my view