The 1996 Billy Zane Phantom film

In the early 16th century, a young boy helplessly witnesses his father killed by Kabai Sengh, the vicious pirate leader of the Sengh Brotherhood, who attacked their ship. The boy jumps overboard and is washed ashore on Bengalla, an Asian island where local tribesmen find him and take him to their village. There he is given the Skull Ring, swears to devote his life to resisting vice and enforcing virtue, and as an adult, adopts the identity of "The Phantom", a masked avenger. The role of The Phantom is passed on from father to son through 400 years, leading people to believe in a single, immortal figure.

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In 1938, Kit Walker, the 21st Phantom, finds Quill leading a group of grave robbers in the jungle. They are searching a burial place for one of the Skulls of Touganda, which grants its owner a tremendously destructive power. The Phantom saves the native boy they kidnapped to be their guide and captures Quill's men, leaving them for the Jungle Patrol to pick up. Revealed to be a Sengh Brotherhood member and the man who killed Kit's father - whose ghost frequently appears to give Kit advice - Quill flees with the Skull and returns to the United States.

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In New York City, Kit's college girlfriend, Diana Palmer, is a frequent traveler whose uncle, Dave Palmer, is the famous owner of the World Tribune newspaper. The paper has been investigating power-hungry businessman Xander Drax, a shady character with a reputation for dealing with criminals. Palmer has uncovered Drax's connection to a mysterious spider web symbol, which he traces back to the Bengalla Jungle. He sends Diana to investigate but makes the mistake of telling New York's treacherous police commissioner, who is allied with Drax, of Diana's trip. Drax's female air pirates led by femme fatale, Sala, hijack the plane; Diana is abducted and taken to their waterfront base in Bengalla. Having been informed of Diana's abduction by the Jungle Patrol's captain, Phillip Horton, the Phantom rescues her and escapes from Quill and his men to his headquarters, the Skull Cave.

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In New York, now dressed as his civilian self, Kit meets with David Palmer at the World Tribune and once again meets with Diana, who has mixed feelings about him since his sudden disappearance several years before. Diana's would-be suitor Jimmy Wells mentions he had seen one of the skulls in the Museum of World History, so Kit and Diana hurry there. Drax and his men capture them, steal the second Skull and unite it with the first, revealing the location of the third Skull on an uncharted island in the Andaman Sea, known as the Devil's Vortex. Kit manages to escape and, as the Phantom, evades the police outside the museum. Meanwhile, after Sala reveals that Diana is the Phantom's girlfriend, she flies Drax, Quill, and Diana to the Devil's Vortex, not knowing that the Phantom has managed to hitch a ride on one of the plane's landing pontoons.

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On the island, Drax meets with the pirate Kabai Sengh, direct descendant of the Brotherhood's original leader, who possesses the third Skull. Sengh warns Drax of the Fourth Skull's existence, which controls the power of the other three. The Phantom appears and battles both men, with Kabai Sengh killed by sharks, and Diana and Sala cooperate to defeat the other villains. Drax unites the three Skulls and turns their power against the Phantom; Quill is accidentally hit and disintegrated in the process. The Phantom uses the Fourth Skull – his own magic ring – to turn the Skulls' power back against them, destroying them and Drax in a powerful explosion. As the energy causes a volcanic eruption, the Phantom narrowly escapes with Diana and Sala.

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Returning to Bengalla, Diana reveals to the Phantom that she has figured out his secret and double identity. Kit removes his mask, telling her that he can only disclose all of his secrets to one person, the woman he intends to marry, but she leaves again for New York. Kit's father laments his son's failure to pursue Diana but states that she will return to the Phantom's jungle, and Kit, one day.

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