Nuclear subs at sea
Even with the plague, there would have to be a number of US nuclear subs out there. They would have been ordered to remain at sea when it broke out. Even if some of them made port before or after the plague got back and those subs were sickened, surely at least a few of them would have been far enough away from land for long enough to not have been infected, and unlike the Nathan James, they would have been in touch with command until there was nobody left.
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