William, the way it was explained to me was that the E-4B served as a communications command post for the National Command Authority, where the President, etc. could stay in contact with assets following the destruction of key locales like the White House, Pentagon, etc. The E-4B would have the ability to communicate Presidential orders to units, but the E-6 Mercury would be responsible for actually issuing commands to Nuclear Assets, as it is able to replicate the authority normally vested in US Strategic Command at Offut AFB.
So the E-4B is a mobile situation room, and the E-6B is a backup Nuclear command post...if that makes sense.
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