Air Force Two was a plane used to transport important officials in the executive branch of the United States government.
It was the plane carrying Cabinet level officials that Dr. Morton Craig attempted to destroy with a missile program he had helped to create and maintain. When Steve destroyed the missile launchers, the pilot of Air Force Two radioed in his sighting of "two large explosions" to a nearby air traffic controller (Target in the Sky).
In real life, "Air Force Two" is the callsign of any United States Air Force craft on which the Vice President of the United States is present. It is not a specific plane, although there is one generally reserved for his or her use. However, neither bionic series makes a specific reference to just what "Air Force Two" is.