The film opens with a recap “For Those Who Came In Late,” narrated by the Phantom's deceased fathe, who appears to his son throughout the film (whether he is a ghost, or simply a figure of the Phantom's memory, is left ambiguous.
Four hundred years ago, a young boy, the last survivor of a pirate attack by the ruthless Sengh Brotherhood, is washed ashore on an island called Bengalla, where he swears to devote his life to the destruction of piracy, greed, cruelty, and injustice. In adulthood, he adopts the identity of “The Phantom”, a masked avenger. The role of the Phantom is passed on from father to son through centuries, causing people to believe in a single, immortal figure and accordingly to nickname him “The Ghost Who Walks” and “The Man Who Never Dies”.
In 1938, Kit Walker, the 21st Phantom, finds the man who killed his father, the mercenary Quill, searching for one of the ‘Skulls of Touganda’, possession of which grants the owner a tremendous destructive power. The Phantom seizes Quill's men and saves the native kidnapped as their guide, but Quill - revealed as a member of the Sengh Brotherhood - retrieves the Skull and returns to the United States of America.
In New York City, Kit's ex-girlfriend, Diana Palmer, is sent by her Uncle Dave to Bengalla in order to investigate claims that businessman Xander Drax , Quill's boss, is resorting to piracy. En route, Diana is captured by female “air-pirates” also obeying Drax, led by Sala. The Phantom, told of Diana's kidnapping by the Jungle Patrol's Captain Phillip Horton, rescues Diana and escapes to his headquarters, the Skull Cave, where Diana meets with Captain Horton and is returned to New York.
The Phantom then travels to New York in civilian guise to meet Diana. There, they locate the second Skull in a museum but are captured by Drax and his men, who steal the second Skull and unite it with the first, revealing the location of the third Skull as an uncharted island on the Yellow Sea. Diana is taken there by Drax, Sala, and Quill, while Kit follows them as the Phantom.
On the island, Drax meets with the pirate Kabai Sengh, a descendant of the Brotherhood's original leader who possesses the third Skull. The Phantom appears and battles both men, with Kabai Sengh killed by his own pool of sharks, as Diana and Sala co-operate to defeat the subordinate villains. Drax unites the three Skulls and turns them against the Phantom (inadvertently killing Quill in the process), only to be destroyed when the Phantom uses the “Fourth Skull” - his own ring - to overcome the others. As the island is consumed in flames, the Phantom narrowly escapes with Diana and Sala.
In parting from Diana thereafter, the Phantom reveals his secret and his double-identity to her with implication that she will, therefore, become his bride, but she leaves again for New York. In the film's closing narration, Kit's father laments his son's failure to pursue Diana but reassures the audience that she will return to the Phantom's jungle, and to Kit, one day.
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