Now I'm curious.
Here is an answer that is helpful though the article is dated. No matter, if anything we should assume that the technology has been updated and much improved.
On 911 immediately after being interrupted during his reading My Pet Goat President Bush was rushed to Air Force One and was airborne ASAP. As far as we know this is one of the most dangerous events we have seen in our lifetime. It would make sense to follow Bush's movements on that day.
Bush and whatever aircraft accompanied AF 1 circled around for a while trying to determine the safest place for the President. The flew around for a while and landed at Barksdale AFB in Louisiana. Barksdale would be a logical place to land due to Barksdale security (they have nukes there and some on the ramp alert ready). Barksdale doesn't mess around.
Bush remained there for a while until it was decided to fly to another very secure base, Offutt, in Nebraska. Offutt previously Strategic Air Command Headquarters (SAC) and now US Strategic Command (STRATCOM) Headquarters. At Offutt all the President needed to monitor and conduct necessary actions were
permanently in place. Security designed and known for its ability to respond to such an incredible event as 911 was well trained and ready within minutes of notification of his arrival.
Here is an article about Bush, AF 1 and what transpired that day. We know from the article that the E-4 that accompanies AF 1 did also land Offutt, as we would expect. I don't know about other accompanying aircraft. What, how many, where did they go, did they remain in the air? Who knows? I doubt the Air Force would like to share that information. At any rate this linked article provides some insight as to AF 1 when the shit hits the fan.
This information might give you some insight,
GIRLPOWER, as to how the US military trains and trains and trains and trains to be prepared for even the unexpected. Constitutionally compliant orders are in place and ready if needed at a moments notice. You practice for it no matter if you're laying in ambush in a cold wet ditch or steaming across or under the sea or responding to alert signals in the air. Every person involved from support to implementation is critical. They are well trained, well disciplined and ready to respond. Everyone depends on everyone to do their job. Those who serve and those who served are very proud of that.