There's almost no certainty that we can stop an ICBM. We have untested systems and untested warning systems that the Soviet Union never even bothered to test. But now there's a rogue nation trying to play tough guy sitting across the Pacific Ocean with nuclear weapons and an experimental ICBM platform.
If an ICBM gets launched, the USA is probably going to throw everything we got to try to stop the missile. Then we'll probably fail, and the city will get nuked anyway. But we gotta do everything within our power to make the probability of success as high as possible.
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San Francisco, Los Angeles, etc. etc. Any of those cities could be lost within a few minutes under these scenarios. If people are saying that this airplane stop-order was over a nuke, I think its actually 100% reasonable to have done these stop-flying orders.