The scenes taking place at "The Institute for New Human Kind" (aka the closed "McKinley Air Force Base" in the film) and of the climactic finale were filmed at the former Williams Air Force Base in Mesa AZ, 30 miles southeast of Phoenix. The base closed in 1993.
The scenes in the diner were filmed at Shep's Diner, which was located on the NE corner of N. Country Club Dr. and W. 2nd St in Mesa, AZ.