More than three decades have passed after Pete "Maverick" Mitchell graduated from TOPGUN. Maverick has avoided promotion to continue flying. Today he is the test pilot of the hypersonic Darkstar prototype. This project is threatened by Admiral Chester "Hammer" Cain, who wants to redirect its funds to developing new drones. Maverick, knowing the jobs of the entire staff are on the line, decides to fly the Darkstar before Cain arrives, achieving the speed of Mach 10 two months before the actual due date. However, being Maverick, he continues to push the prototype past Mach 10 until it disintegrates around him.
Cain, despite wanting to ground Maverick for his actions, instead sends him to NAS North Island under orders from Maverick's old rival-turned-friend, Tom "Iceman" Kazansky, now a Four-Star Badass and COMPACFLT (Commander, U.S. Pacific Fleet
), there to train students again.
As part of a mission to bomb a secret uranium refinery that is deemed a threat to the United States, Maverick is called upon ordered to train a group of TOPGUN graduates, assembled by Vice Admiral Beau "Cyclone" Simpson and Rear Admiral Solomon "Warlock" Bates. The latter is largely supportive of Maverick, but the other dislikes Maverick's, uh, Military Maverick style; that said, the Old Soldier is the only pilot in the Navy who has practical experience with everything this mission will involve. The plant is hidden deep in a canyon and is guarded by SAM missiles and several enemy aircraft, particularly Bland-Name Product "5th-generation fighters" (Sukhoi Su-57s, NATO reporting name "Felon") which can outfly the Navy's current front-line fighter, the F/A-18 Super Hornet. As such, the Airstrike Impossible will be a Stealth-Based Mission: two pairs of F/A-18s will fly through the canyon to drop bombs on the plant, pull a very high climb to escape, and then attempt to dodge their way out of a Macross Missile Massacre of defensive SAM sites — all while avoiding the 5th-gen fighters.
The pilots include cocky Lieutenant Jake "Hangman" Seresin; LT Natasha "Phoenix" Trace and her Guy in Back Robert "Bob" Floyd; and LT Bradley "Rooster" Bradshaw, the son of Maverick's late friend Goose. The pilots typically work in trios: the lead plane flies a one-seat F/A-18E and carries the bombs; the trailing plane, an F/A-18F, serves as a Target Spotter, via an aiming laser controlled by the Guy In Back, to guarantee the Player-Guided Missile hits its target.
During the training, a rivalry forms between Hangman and Rooster due to their Red Oni, Blue Oni contrast; Hangman, the only Naval aviator to score a kill this century, is impulsive and selfish, while Rooster, despite a proven pedigree and clear ability, is stricken by Paralysis by Analysis. Meanwhile, Maverick meets his former girlfriend Penny Benjamin, who now owns a bar called "The Hard Deck". He tells Penny that he wanted to keep his promise to Goose's late wife Carole to keep her son from flying, which resulted in him blocking Rooster's application to the Naval Academy and setting back his career. He later meets with Iceman, who has throat cancer and has difficulty communicating, using his computer to type to Maverick before struggling to form a few words. After some flirting, Maverick and Penny close their Relationship Revolving Door with an emphatic Relationship Upgrade.
As Maverick's training pushes through to mixed results, Kazansky passes away. Almost immediately after, Cyclone fires Maverick and designs a new plan to strike the enemy base which is much easier to execute but carries a concomitant higher risk of getting shot down. Maverick makes an unauthorized flight following his own plan and becomes the first person to actually succeed at executing it; Cyclone reluctantly appoints Maverick as flight leader. At the Hard Deck later that night, Maverick turns up in full dress uniform and quietly shares the news with Penny, and the two share a poignant goodbye on the beach outside.
To actually execute the mission, Maverick pairs himself with Phoenix and Bob, while Rooster is paired with Payback and his WSO Fanboy. Hangman and the other five pilots are put on standby. The Navy launches Tomahawk missiles to destroy the enemy's air base before attacking the plant; this prevents the Navy flight from having to deal with reinforcements, but two 5th-gen fighters are already in the air and immediately set out for the plant to find out what's going on. Despite the harrowing circumstances, the attack is successful and the plant is destroyed; but, as expected, the Naval pilots are attacked by surface-to-air missiles during egress. When Rooster runs out of countermeasures and is unable to shake the missiles on his tail, Maverick performs a Heroic Sacrifice to save Rooster and is forced to eject. Once Maverick regains consciousness, he is promptly spotted and attacked by a Hind-D gunship, which is shot down by Rooster, who disobeyed orders to retreat; he too is shot down in turn. Maverick is irritated to have his Heroic Sacrifice negated, but allows that he is glad to see the closest thing he has to family.
When Maverick was first briefed about this mission, Warlock mentioned that the air base is stocked with, in addition to at least 3 Su-57s, several old F-14 Tomcats from the batch that were sold to Iran in The '70s. Maverick and Rooster contrive to steal one of them to escape, but once they are in the air, they are confronted by the two Su-57 Felons. Despite flying a plane at some 50 years older and in disrepair, and despite having to deal with jaw-dropping aerial maneuvers which showcase why everyone's so freaked out about these newer 5th-gen fighters, Maverick engages with both hostiles and succeeds at blowing both away.
As the F-14 heads out to sea, it is confronted by a third and final Felon that they are unable to shoot down due to being out of ammunition. Even better, the Ejection Seat doesn't work either. All seems lost... But The Cavalry arrives in the form of Hangman, who shoots it down while it is focused on attacking Maverick and Rooster. Maverick, Rooster, and Hangman return to the carrier and are welcomed as heroes; Rooster and Hangman reconcile, as do Maverick and Rooster.
In the last scenes of the film Maverick and Rooster work on a P-51 Mustang and Maverick reunites with Penny and her daughter Amelia. Maverick takes Penny for a ride in his P-51 while Rooster posts a photo of their success next to a photo of his late father with Maverick.
