Over 30 years after graduating from Top Gun,^[a] United States Navy Captain Pete "Maverick" Mitchell is a test pilot. Despite Maverick's many distinguished achievements, repeated insubordination has kept him from flag rank.^[b] His friend and former Top Gun rival, Admiral Tom "Iceman" Kazansky, is commander of the U.S. Pacific Fleet and often protects Maverick from being grounded. Rear Admiral Chester "Hammer" Cain plans to shut down Maverick's hypersonic "Darkstar" scramjet program in favor of funding drones. To save the program from cancellation, Maverick changes the flight plan in the upcoming test from the Mach 9 to Mach 10 to meet the program's contract specification. However, the prototype is destroyed when Maverick pushes beyond Mach 10. Iceman again saves Maverick's career by sending him to NAS North Island for his next assignment, but Hammer warns Maverick that the era of crewed fighter aircraft will soon end.

The Navy has been tasked with destroying an unsanctioned uranium enrichment plant, which sits in a valley at the end of a canyon. It is defended by SA-3 Goa surface-to-air missiles (SAMs), GPS jammers, and what appear to be fifth-generation Sukhoi Su-57^[c] fighters as well as previous-generation F-14 Tomcats. Maverick devises a plan to attack with two pairs of F/A-18E/F Super Hornets. He learns that he will not take part in the strike; instead, he is to train an elite group of Top Gun graduates assembled by Air Boss Vice Admiral Beau "Cyclone" Simpson.

Maverick out-dogfights his skeptical students to win their respect. Lieutenants Jake "Hangman" Seresin and Bradley "Rooster" Bradshaw—son of Maverick's late best friend and RIO Nick "Goose" Bradshaw—clash. Rooster dislikes Hangman's cavalier attitude, while Hangman criticizes Rooster's cautious flying. Maverick reunites with former girlfriend Penny Benjamin, to whom he reveals that Rooster's mother made him promise before she died that Rooster would not become a pilot. Rooster, unaware of the promise, angrily resents Maverick for impeding his military career and blames him for his father's death. Maverick is reluctant to further interfere with Rooster's career, but the alternative is to send him on the extremely dangerous mission. He tells his doubts to Iceman who has terminal throat cancer. Before dying, Iceman advises that "It's time to let go" and reassures him that both the Navy and Rooster need Maverick.

With Maverick's protector gone, Cyclone removes him as instructor following a training incident in which an F/A-18 is lost. Cyclone relaxes the mission parameters so they are easier to execute but allow the enemy jets to catch the team. During Cyclone's announcement, Maverick makes an unauthorized flight through the training course with his preferred parameters, proving that it can be done. Cyclone reluctantly appoints Maverick as team leader.

Maverick flies the lead F/A-18E in the strike package, accompanied by a buddy lazing F/A-18F^[d] flown by Lieutenant Natasha "Phoenix" Trace and WSO Lieutenant Robert "Bob" Floyd. Rooster leads the second strike pair, which includes Lieutenant Reuben "Payback" Fitch and WSO Lieutenant Mickey "Fanboy" Garcia. The four jets launch from an aircraft carrier, and Tomahawk cruise missiles destroy the nearby air base as they approach. The teams successfully destroy the plant but the SAMs open fire during their escape. Rooster runs out of countermeasures, and Maverick sacrifices his F-18 to protect Rooster. Believing Maverick to be killed,