The ending of Thunderball settles on the Disco Volante, where Domino kills Largo, the yacht is destroyed and Bond and Domino are pulled from the sea. Domino's killing of Largo completes her arc after she learns he caused her brother's death.
She spends the middle of the film as a woman Bond must win over, and the turning point comes when she discovers what Largo did. Her kill is the payoff of that discovery, so the ending belongs to her as much as to the hero.
The set piece around it has several moving parts. Earlier, Bond explores the seabed and finds evidence of where the bomber went down; that search is what sets up the finale, because it proves the bombs were moved and sends the hunt to Largo's yacht. Then a large force of divers attacks the Disco Volante, a fierce underwater battle follows, and Bond boards the vessel and fights Largo. The action is spread across water and deck, and it is the work that earned John Stears his Oscar for Special Visual Effects. The Academy's record of the 38th Academy Awards, held on 18 April 1966 at the Santa Monica Civic Auditorium, confirms the win.
The bombs are recovered, so the ransom plot fails. SPECTRE stays active as Bond's enemy, so the organization survives even though Largo and his yacht do not. The film sets up no direct follow-up story, which is how it differs from a serial structure: the next film, You Only Live Twice, starts from SPECTRE still being a threat rather than from any unresolved plot thread here.
The following comparison is opinion. Thunderball is the fourth film in the official series, after Goldfinger, and its finale moves the climax from land to open water. Count Lippe is the only SPECTRE face at the start, at the health clinic, while Largo is the face at the end, so the villain's exposure grows from one hidden agent to a yacht commander with a crew and a fleet of divers. Domino's role in that climax also differs from a typical rescue: she ends the fight rather than waiting for Bond to end it. The unofficial, non-EON film Never Say Never Again retells the same story, but this ending belongs to the official 1965 film directed by Terence Young.
The numbers back up the scale of the production: Thunderball cost $9 million and earned $141.2 million worldwide, according to The Numbers. A budget that size paid for a climax built around a yacht, a mass dive assault and a long sea fight.