At Fort Sonora, a U.S. Army Supply Group in the Philippines, a new recruit named Joe watches fellow soldiers kick a “hacky sack,” but declines to join them. Sometime later, Colonel Hickock bids farewell to his daughter, Patricia, and sends her to the airport under protection of Sergeant Rinaldo and a convoy of soldiers. On the way, a Philippine militia group, posing as a road construction crew, ambushes the convoy at gunpoint. Patricia escapes as the U.S. soldiers fight back. A mysterious figure named Black Star Ninja watches from a hillside and sends his ninja army to join in the fight, killing men from both sides. Joe rescues Patricia and flees into the jungle. The Army survivors return to the base and report that Joe is to blame for the casualties because he instigated retaliation. Declaring that a second group, the ninjas, attacked them, the Army becomes aware of a new threat. Meanwhile, Black Star Ninja is impressed with Joe’s skills and reports back to his boss, a black market arms dealer named Ortega, reporting that the “American ninja” foiled their attack. Joe returns Patricia safely to the Army base, but is reprimanded for his participation in the fight. The colonel reviews Joe’s file and discovers he has a history of violent behavior, and suffers from amnesia. Around the base, the soldiers treat Joe as an enemy, and blame him for the death of four soldiers. As Joe rests, he remembers being trained in martial arts as a boy. Elsewhere, a prospective weapons buyer visits Ortega at his vast estate, which includes a ninjutsu training ground. Back at the Army base, a soldier named Jackson provokes a fight with Joe. Using his martial arts skills, Joe wins the brawl, impresses the others, and ultimately befriends Jackson. When asked about his training, Joe tells Jackson that he has amnesia and sees only flashes of his past. Attracted to Joe, Patricia schemes to lure him to a restaurant. There, Sergeant Rinaldo and Ortega see the couple. Realizing who Patricia’s date is, Ortega orders Rinaldo to kill Joe for interfering with their arms dealing. Sometime later, Rinaldo sends Joe to the Army supply warehouse. Sensing something amiss, Joe comes under attack from Ortega’s ninjas, but fights them off. As his supply truck is stolen, Joe hides underneath the vehicle and rides to Ortega’s compound, and witnesses the illegal dealings happening there. When Joe is spotted, another fight ensues. Ortega’s gardener, Shinyuki, aids in Joe’s escape, and hints that they know each other. Later, Joe returns to the Army base and is promptly imprisoned for allegedly stealing the supply truck. Jackson unsuccessfully appeals to Rinaldo for Joe’s release, then goes to Patricia and the colonel for help. However, Colonel Hickock believes Joe is at fault. Elsewhere, ninjas break into the military jail to kill Joe at Ortega’s behest. A fight ensues and Joe escapes. He makes his way to Jackson and shares his knowledge of the sergeant and Ortega’s misdeeds. Despite Joe’s objections, Jackson persuades Joe to share what he knows with the colonel. At Colonel Hickock’s house, Joe is threatened with a second arrest, but jumps through a window and escapes in a truck as the military police give chase. Rinaldo’s Jeep runs off the road and explodes. Revealing his involvement in the stolen missiles plot, Colonel Hickock invites Ortega to his home to discuss Joe’s interference. As the two men argue, Hickock decides to call off the plan. Upstairs, Black Star Ninja sneaks into Patricia’s room and kidnaps her. When Joe later returns to Ortega’s compound, he encounters Shinyuki, who reveals that he found Joe as a baby and taught him to be a ninja. One day, an explosion caused Joe’s amnesia, and he was separated from Shinyuki. In turn, Shinyuki allowed Joe to forget his past until he was ready to know his true identity. Shinyuki then presents an array of ninja weapons and reminds Joe of the ninja code. Joe agrees to honor the code and refers to Shinyuki as “father.” Since Black Star Ninja has taken a malicious path, Shinyuki and Joe agree he must die. When daylight breaks, a helicopter arrives on Ortega’s estate to transport the stolen missiles. Joe, dressed as a black-masked ninja, attacks, and a fight ensues. Ortega reveals that he is holding Patricia hostage and hopes Joe will surrender. The fight continues, with Shinyuki coming to Joe’s aid. The two ninjas battle Ortega’s army and Shinyuki is killed. Army tanks, led by Jackson, arrive as Ortega tries to get away with Patricia in the helicopter. However, Colonel Hickock attempts to rescue his daughter, and is shot dead by Ortega. Joe kills Black Star Ninja and leaps onto the helicopter landing skids as it lifts off. Battling with Ortega in midair, Joe grabs Patricia, and jumps to a rooftop. Jackson shoots a missile to blow up the helicopter, as Joe removes his mask.