Now promoted to Army Rangers, Joe Armstrong and Curtis Jackson find themselves sent to a secluded Caribbean island to assist the Marine Corps in uncovering the mystery behind the vanishing soldiers. They are briefed by their commanding officer, "Wild Bill" Woodward, who informs them that four marines have been captured, but details about their captors remain elusive, leaving terrorism out of the equation. The only witness, a boy named Toto, has seen two soldiers being attacked by a gang before being taken away by a group of men clad in black.
On arrival, Charlie McDonald invites the duo to indulge in water skiing. However, Tommy Taylor, their boat driver, secretly sabotages their vessel. Sensing danger, Joe chooses to stay onshore, while Curtis joins in the swimming. Almost immediately, Joe is ambushed by Ninjas but is saved just in time by Curtis. Although their initial report is disregarded, Woodward allows them a week to pursue their investigation. During a phone call with the Lion, Tommy is instructed to set a trap for Armstrong, detailing a rendezvous point at the Blind Beggar Bar.
Joe confronts a gang similar to the one that took the soldiers and soon learns about a notorious drug dealer, The Lion. He is the wealthiest individual on the island and utilizes his drug fortune to fund dubious research on his private property, known as Blackbeard Island. After informing Wild Bill about their findings, the men learn from Taylor that Blackbeard Island is officially owned by Professor Sanborn. Eager to investigate, Wild Bill invites them to the governor's ball.
At the ball, Inspector Singh quickly accuses Joe of being involved in Taylor's death. Joe manages to discover that a man named Leo Burke is associated with Singh and is, in fact, The Lion himself. After a girl named Alicia Sanborn is kidnapped during the event, Wild Bill grants Joe and Curtis permission to rescue her. Alicia informs them that Burke has kidnapped her father, but the authority figures dismiss her claims.
Joe, Curtis, and Charlie pursue the kidnappers into the Blind Beggar's Bar, where they engage in a fierce battle with the local gang before making their escape. The group concocts a story to evade Inspector Singh's inquiries. Joe uses Toto's assistance to track down Alicia, but they are once again assaulted by Ninjas. With bravery and skill, Joe takes out the attackers on his own, aided by a truck-driving Toto. However, one Ninja manages to board their vehicle. In a moment of ingenuity, Joe instructs both Toto and Alicia to leap from the vehicle just before it crashes into gas cans, resulting in a massive explosion that dispatches the Ninja.
As Joe and Alicia head towards the boats, Joe tasks Toto with relaying a message to Wild Bill to inform him of their journey to Blackbeard Island. They must wait for nighttime to navigate around the patrol guards in the waters. During this time, Alicia shares that her father had been working on a significant cancer cure before his research was taken over by Burke, who intends to utilize it to create an army of super Ninjas. The kidnapped marines are part of this dark experiment.
While waiting for an order to proceed from the ambassador, Curtis and the rest of the marines remain at the base, meaning Joe and Alicia are on their own. Upon reaching the island, they infiltrate the lab in Ninja attire just as Burke unveils his Super Ninja program. They succeed in rescuing Professor Sanborn, who reveals where the captured marines are held. As they make their escape, they are ambushed and face a fierce battle against the Ninjas. Although they initially hold their ground, the tide turns against them, leaving only two marines alive after a brutal confrontation.
In a courageous retaliation, the marines attack the base, exposing the governor and Inspector Singh as accomplices in Burke's malevolent plans. In the end, the governor is apprehended by Wild Bill, while Singh's fate remains uncertain. Professor Sanborn confronts Burke and detonates a remote-control bomb, obliterating his Super Ninja program, resulting in the demise of both men. The movie culminates with Joe Armstrong engaging in a final showdown with Tojo Ken, triumphantly defeating him before the marines celebrate their victory and bid farewell to their island friends as they prepare for their return to America.
