United States Naval Aviator Lieutenant Pete "Maverick" Mitchell (Tom Cruise) flies the F-14A Tomcat off USS Enterprise (CVN-65), with Radar Intercept Officer ("RIO") Lieutenant (Junior Grade) Nick "Goose" Bradshaw (Anthony Edwards). At the start of the film, wingman "Cougar" (John Stockwell) and his radar intercept officer "Merlin" (Tim Robbins), intercept MiG-28s over the Indian Ocean. During the engagement, one of the MiGs manages to get missile lock on Cougar. While Maverick realizes that the MiG "(would) have fired by now", if he really meant to fight, and drives off the MiGs, Cougar is too shaken afterward to land, despite being low on fuel. Maverick defies orders and shepherds Cougar back to the carrier, despite also being low on fuel. After they land, Cougar retires ("turns in his wings"), stating that he has been holding on "too tight" and has lost "the edge", almost orphaning his newborn child who he has never seen. Although disapproving of Maverick's reckless flying and repeated violation of rules, the Enterprise's Commander, Air Group "Stinger" (James Tolkan) sends him and Goose—now his top crew—to attend the Top Gun school at NAS Miramar.
Maverick flies recklessly partially because of his father, Duke Mitchell, a Naval Aviator with VF-51 aboard the USS Oriskany (CV-34) during the Vietnam War. The elder Mitchell died on November 5, 1965 when his McDonnell Douglas F-4 Phantom II was shot down, and the official story, which Maverick refuses to believe, is that Duke made a mistake. Goose is cautious and devoted to his wife, Carole (Meg Ryan), and child. The two officers are nonetheless close friends and effective partners, with Goose as the only family Maverick has. At a bar the day before the Top Gun program starts, Maverick, assisted by Goose, unsuccessfully approaches a woman by singing "You've Lost That Lovin' Feelin'". He learns the next day that she is Charlotte "Charlie" Blackwood (Kelly McGillis), an aeronautical engineer and civilian Top Gun instructor.
Maverick's reckless flying both annoys and impresses Lieutenant Commander Rick "Jester" Heatherly (Michael Ironside) and other instructors. He defeats Jester in combat, but violates two rules of engagement in the process. He continues to pursue Charlie and becomes a rival to top student LT Tom "Iceman" Kasansky (Val Kilmer)—who considers Maverick's methods dangerous and unsafe. Although outwardly critical of Maverick's tactics, Charlie eventually admits that she admires his flying but was critical because she was afraid for her credibility. They begin a romantic relationship.
During one flight, Maverick breaks off from his wingman "Hollywood" to go one-on-one with chief instructor Commander Mike "Viper" Metcalf (Tom Skerritt), described as "the (finest) fighter pilot... in the world". Although Maverick matches the older pilot move for move, Viper lasts long enough for Jester—who has defeated Hollywood off-screen—to maneuver around and "shoot" Maverick down, demonstrating the value of teamwork over individual ability.
Near the end of the program, Maverick and Iceman both chase Jester, the latter attempting to gain a missile lock on the target. Under intense pressure from Maverick, Iceman breaks off. Maverick's F-14 flies through the jet wash of Iceman's aircraft and suffers a flameout of both engines, entering a flat spin from which he cannot recover, forcing him and Goose to eject. Goose ejects directly into the jettisoned aircraft canopy and breaks his neck, dying instantly.
Although the board of inquiry clears Maverick of responsibility, he feels guilty for Goose's death, losing his aggressiveness when flying. Charlie and others attempt to console him, but Maverick considers leaving the Navy. Unsure of his future, he seeks Viper's advice. Viper reveals that he served with Maverick's father in VF-51, and discloses classified details, explaining how Duke stayed in the fight after his F-4 was hit and saved three planes before he died. During the graduation party, Iceman, Hollywood, and Maverick are ordered to immediately report to Enterprise to deal with a "crisis situation", providing air support for the rescue of a stricken communications ship, the SS Layton, that has drifted into hostile waters. Maverick and Merlin are assigned to one of two F-14s as back-up for those flown by Iceman and Hollywood, despite Iceman's reservations over Maverick's state of mind. In the subsequent hostile engagement with six MiGs, Hollywood is shot down but manages to eject; Maverick is sortied alone due to catapult failure and nearly retreats after encountering circumstances similar to those that caused Goose's death. Upon finally rejoining Iceman, they shoot down four MiGs and force the others to flee, and return triumphantly to Enterprise. Offered any assignment he chooses, Maverick decides to return to Top Gun as an instructor (which Stinger jokingly expresses horror at the thought of).
Sitting alone in a restaurant in downtown San Diego, Maverick hears "You've Lost That Lovin' Feelin'" playing on the jukebox and recalls meeting Charlie. She enters the bar and the two reunite.
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