Coincidentally, Russia was also in the midst of its own nuclear war exercise on 9/11. When Russian intelligence detected signs the United States was preparing to move to DEFCON 3, President Vladimir Putin urgently tried to reach President Bush to clarify what was happening.
For 30 minutes, the White House communications office tried but failed to establish a secure link between Air Force One and the Kremlin. National Security Advisor Condoleezza Rice (who speaks Russian), finally got on the phone with President Putin to arrange a mutual stand-down.
Because Secretary of Defense Donald Rumsfeld had ordered US forces worldwide to move to DEFCON 3, officers aboard our ballistic missile submarines on alert began working through their checklists to prepare for a possible launch, including opening locked safes to remove and review nuclear war plans.
In the midst of all that, NORAD and the FAA were implementing SCATANA (Security Control of Air Traffic and Navigation Aids), an emergency plan developed in the 1960s to ground all non-military aircraft in US airspace that was intended for use only in case of an all-out nuclear war.
At 9:25 AM EDT, all aircraft nationwide not already airborne were grounded, and those in the air were ordered to return to their point of origin or land at a nearby airport. By 2:07 PM, all domestic flights were grounded, and by 5:30 PM, all international flights were on US or Canadian soil.
Until September 11, 2001, SCATANA—which was developed to provide unrestricted airspace for US bombers and ballistic missiles—had never been fully implemented, although it was partially activated on November 9, 1979, during a very serious nuclear false alarm originating at NORAD.
In fact, only a modified version of SCATANA was implemented on 9/11: all civilian aircraft were grounded, but ground navigation aids were not turned off (as they would have been during a nuclear attack), allowing planes to safely navigate to their new and unexpected destinations.
Many lessons were learned, ie about the PEOC limitations. With what appears to be a network of advanced hardened deeply buried protective structures built in the decades since.