The Germans have no destroyer present, therefore the defending air units can not hit the sub, and of course the sub can never hit planes. Think of it in terms of the combined arms rule, air units can only hit subs if they are combined with at least 1 participating destroyer, the difference with this particular combined arms is that it works while attacking and defending. In the scenario that you described, the sub would destroy the remaining transport without rolling and the defending fighters can do nothing.
Rules question about subs and transports
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So Japan has 2 transports and 3 subs in a sz, and the US has a cruiser within range of this Japanese fleet. Since warships can ignore the presence of subs, can the cruiser attack the transports? Or because there is a battle in that sz, will the cruiser have to fight the subs?
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A naval combat would be initiated. The player owning the subs would then have to decide if they wanted to submerge or not. If they don’t, the cruiser would have to fight the subs first.
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Since warships can ignore the presence of subs, can the cruiser attack the transports?
I believe they can only ignore subs during non combat movement.
On the other hand, subs can always choose to ignore surface ships as long there is no destroyer present
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If an attacker without a DD initiates combat in a zone with a defending sub, the owner of the sub decides whether or not to submerge it, which removes the subs from combat.
Any remaining units in the combat will then proceed to be rolled normally.
As the attacker with the cruiser, you should be aware that the defender can pick either option with the subs.
That subs don’t block movement is a separate feature of submarines - another one of the several special rules that apply only to subs.
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Also, assuming the cruiser initiates combat and the defending subs remain, don’t forget that the defending subs get to shoot first even though they are defending. That means the cruiser might not even get to shoot at all…
Marsh





