US Naval Aviator Lieutenant Pete "Maverick" Mitchell and his radar intercept officer (RIO) Lieutenant (junior grade) Nick "Goose" Bradshaw, stationed in the Indian Ocean aboard the USS Enterprise, fly the F-14A Tomcat. During an interception with two hostile MiG-28s,^[a] Maverick missile-locks on one, while the other hostile locks onto Maverick's wingman, Cougar. Maverick drives it off, but Cougar is so shaken that Maverick defies orders to land and shepherds him back to the carrier. Cougar resigns his commission. Maverick and Goose are sent in his place by CAG "Stinger" to attend Top Gun, the Naval Fighter Weapons School at Naval Air Station Miramar.

Prior to the first day of instruction, Maverick unsuccessfully approaches a woman at a bar. He learns the next day she is an astrophysicist and civilian Top Gun instructor Charlotte "Charlie" Blackwood. She becomes interested in Maverick upon learning of his inverted maneuver with a MiG-28. In Maverick's first training hop, he defeats instructor Lieutenant Commander Rick "Jester" Heatherly, but to do so, he flies below 10,000 feet (3,000 m), breaking a major rule of engagement. Maverick and Goose also buzz the control tower when specifically told not to do so. They are reprimanded by chief instructor Commander Mike "Viper" Metcalf.

Privately, Jester tells Viper that while he admires Maverick's skill, he is not sure if he would trust him as a teammate in combat. In class, Charlie objects to Maverick's aggressive tactics against the MiG-28, but privately tells him she admires his flying; they begin a romantic relationship.

On training Hop 19, Maverick abandons his wingman "Hollywood" to chase Viper. As a result, first Hollywood and then Maverick are defeated in a demonstration of the value of teamwork. Jester tells Maverick his flying is excellent, but criticizes him for leaving his wingman. Maverick’s rival, Lieutenant Tom "Iceman" Kazansky calls his behavior "foolish", "dangerous" and worse than the enemy, to which Maverick responds “I am dangerous”.

Maverick and Iceman, the leading contenders for the Top Gun Trophy, chase an A-4 in Hop 31. As Iceman has trouble getting a lock on the A-4, Maverick pressures him to break off so that he can move into firing position. However, Maverick's F-14 flies through Iceman's jet wash and suffers a flameout of both engines, going into an unrecoverable flat spin. Maverick and Goose eject, but Goose is killed when his head slams into the jettisoned aircraft canopy.

The board of inquiry clears Maverick of any wrongdoing, but he is shaken and guilt-ridden, and considers quitting. He seeks advice from Viper, who flew with Maverick's father in the Vietnam War-era air battle where he was killed. Contrary to official reports faulting Mitchell, Viper says he died heroically. He tells him he can succeed if he regains his self-confidence. Maverick chooses to graduate and congratulates Iceman, who has won the Top Gun Trophy. Iceman, Hollywood, and Maverick receive immediate deployment orders to deal with a crisis situation; they are sent to the Enterprise to provide air support for the rescue of the SS Layton, a disabled communication ship that drifted into hostile waters.

Aboard Enterprise, Iceman and Hollywood are assigned to provide air cover, with Maverick and RIO Merlin on standby. Iceman expresses his concerns to Stinger about Maverick's mental state, but is told to just do his job. Iceman and Hollywood are pulled into a dogfight with what first appear to be t