You need to use a FOB to access the navigation computer.
The FOB needed to access the navigation computer.
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To get into the Commanders office you can Attack on sight, sneak into, or lie to the guard and simply walk in posing as the cleaning crew.
Then head to the tanker in San Francisco and on the lower level of the tanker use it to go to Control station Enclave. Be warned once you do use it, you can not come back to the wasteland until the game has been beaten.