If Air Force One is flying over potentially dangerous territory, it's accompanied by a mysterious jet known only as 'the doomsday plane,' which follows at a safe distance. It's a stealthy 747 which looks out for incoming threats, or unforeseen circumstances like a meteor strike.
The plane has been engineered to remain in the sky for days if it has to, and can also outrun a nuclear explosion. If the ground isn't safe to land on, it will keep the President in the sky.