From http://en.wikipedia.org/wiki/Hot_Shots!:

Hot Shots has been described as “Top Gun meets Airplane!”. The film begins at Flemner Air Base 20 years prior. A pilot named Leland “Buzz” Harley (Bill Irwin) loses control of his plane and ejects, leaving his co-pilot Dominic “Mailman” Farnum (Ryan Stiles) to crash alone; although Mailman survives, he’s mistaken for a deer owing to the branches stuck to his helmet and is shot by a hunter. Topper Harley (Charlie Sheen) wakes up from a nightmare he’s having about the event when Lt. Commander Block (Kevin Dunn) asks him to return to active duty as a pilot in the U.S. Navy. This poses a dilemma for Harley, as he previously left the Navy to live with Native Americans.

Harley becomes romantically involved with his therapist, Ramada (Valeria Golino), although she’s already involved with another fighter pilot (Cary Elwes), who hates Topper because of the loss of his father “Mailman” to Buzz Harley (and believes Topper may do the same to him). Amid the chaos, the owner of an aerospace firm is trying to sabotage the mission in order to make the current fighter jets look bad in hopes that the Navy will replace them with his German-made jets. However, Topper Harley successfully completes the mission to destroy a nuclear power plant despite his jet’s malfunctioning armament.

Wasn’t Hot Shots! a Top Gun parody in the same vein as Naked Gun?

Hot Shots!, in addition to being a parody of war movies—particularly Top Gun—is a story of the archetypal conflict of self vs. self.

Ace navy pilot Topper Harley’s father was blamed for the death of another pilot nearly 20 years before the movie takes place. Topper, who is somewhat mentally unstable, freezes up at the mere mention of his father. He projects his father’s failures onto himself.

Topper Harley’s greatest enemy in the film is not his rival Lt. Kent Gregory or the Iraqi air force, but his own self-doubt.