My guess is that its "Parts: The Clonus Horror." When the main clone guy escapes from the clone farm, he is shot at repeatedly while running away through a desert-like setting. It's one of the many things that Mike, Crow, and Servo heckled in the MST3K episode of "Parts."
Look at the scene about five minutes into the film on this clip from the aforementioned MST3K episode, see if that's it:
No fighter jets are involved however.... so I'm probably wrong.