Two weeks before Johnny's 16th birthday, ninjas attack the teenagers, but they are defeated by Zatch, a mysterious warrior with an eye patch.

Zatch reveals to Johnny and Adam that they are actually the sons of the king of Patusan, whose land and monarchy was overthrown by the evil Colonel Chi when the boys were young.

They reach Patusan and discover what Colonel Chi's rule has wrought, including a burned village and a chain gang of political prisoners.

Rallying the villagers, they travel to the coast, opposite from an island that houses the royal city and Colonel Chi's dungeon.

Landing on the island, Johnny and Zatch lead the attack on the royal city, taking down Chi's henchmen and freeing Mac.

Johnny confronts Colonel Chi, successfully defeating him by knocking him into a body of water with the help of Adam and his Game Gear.

Over its opening weekend, the film grossed $2 million,[1] placing 13th in box office rankings, ahead of Manhattan Murder Mystery.

Voedisch considered Rob Schneider's presence as comic relief unfunny, believing that Leslie Nielsen should have received more screen time as the dictator.

Sherman admired the story arc in which the protagonists learn to accept their destinies, but he thought that "the manufactured thrills along the way get obnoxious".

[18] Desmond Ryan of The Philadelphia Inquirer thought that Leslie Nielsen was deceptively portrayed in a major role similar to that of Lieutenant Frank Drebin from The Naked Gun films, instead having merely "a running and unfunny gag about his malfunctioning answering machine and generally wasted otherwise".

[19] Mick LaSalle of the San Francisco Chronicle considered the story of Surf Ninjas to be "harmless and painfully dull".

Piccoli compared the martial arts choreography in the film to the "cartoon fantasies that little boys re-enact on neighbors' lawns: the good guys, alone and outnumbered by the charging horde, air-punch their way to glory".

[21] Ron Weiskind of the Pittsburgh Post-Gazette perceived Reyes, Jr. as "a likable presence on screen" and Schneider to be occasionally humorous in his series of gaffes.

[22] Joe Holleman of the St. Louis Post-Dispatch thought that Surf Ninjas pushed "the right buttons to guarantee adolescent enjoyment".

Holleman acknowledged that the film was "not exactly a milestone in cinematic achievement", but he applauded the acrobatic choreography and the delivery of Schneider's throwaway lines in "the movie's funniest moments".

[23] Sean P. Means of The Salt Lake Tribune described the film as a Toys "R" Us version of Indiana Jones and the Temple of Doom, with "the cartoonish martial-arts sequences [owing] their entire existence to the villains' stupidity".