The plot culminates in the perilous mission against the uranium enrichment facility. Maverick, reinstated as team leader, flies with Phoenix & Payback and Rooster & Bob as the two attack pairs. They successfully destroy the target, but during the chaotic escape, Maverick's F/A-18 is shot down by a surface-to-air missile as he draws fire away from Rooster. Believing Maverick to be killed in action, the team is ordered back to the carrier. However, Rooster disobeys orders and turns back, spotting Maverick alive on the ground but under fire from an enemy gunship. Rooster destroys the gunship but is himself shot down.
Reunited on the ground, Maverick and Rooster find an old F-14 Tomcat—the same type of plane from the original film—at the enemy's damaged airbase and manage to get it airborne. In a thrilling dogfight, they are engaged by two advanced fifth-generation enemy fighters. Outmatched technologically, they rely on pure skill to shoot down both jets. Just as a third enemy fighter appears and they are out of countermeasures, Hangman—who was the reserve pilot—arrives just in time to shoot down the final threat, saving them. Back on the carrier, Maverick and Rooster finally reconcile, their shared ordeal having erased all animosity. Rooster acknowledges Maverick's difficult position regarding his career and father's legacy. The film ends with Maverick peacefully working on his P-51 Mustang before taking Penny Benjamin for a flight, signifying he has found closure and is ready for a new future.