Every summer, the Douglas brothers—Samuel Max Elliott Slade, 12, Jeffrey Chad Power, 11, and Michael Michael Treanor, 6—visit their grandfather Mori Tanaka Victor Wong at his cabin, where Mori teaches them the art of ninjutsu. As the season winds down, Mori assigns each boy a new “ninja” name that reflects his personality: Samuel becomes Rocky, Jeffrey becomes Colt, and Michael becomes Tum-Tum. The trio soaks up training with curiosity, learning to move with quiet focus and to see danger from a distance, all under Mori’s patient guidance.
Back home, the brothers’ father, Sam Douglas, an FBI agent, orchestrates a sting operation to trap a master criminal named Hugo Snyder Rand Kingsley in a weapons deal. Snyder slips the net using his ninja henchmen and escapes by helicopter. He later confronts Mori, his former partner, and tests him with a squad of ninjas. Mori holds his ground, aided by his grandsons, and defeats the intruders. In a tense face-to-face, Snyder fails to persuade Mori to train his men and even threatens Mori’s family if the grandfather doesn’t urge Sam to drop the pursuit.
When the boys return to their ordinary lives, their father’s reaction is cool at best—he’s unimpressed by their new names and what they’ve learned. Emily, Rocky’s friend, admires his new moniker and agrees to ride with them to school the next day, signaling a normal summerday that might soon collide with danger.
Snyder hatches a plan to kidnap the brothers and use them as leverage against Sam to seal his missile deal. His consigliere Nigel Brown coordinates with reckless underlings and crusty accomplices like Fester and his crew, but their operation is briefly interrupted by FBI activity. The next morning, Fester and friends shadow the brothers on their way to school, only to be distracted by a minor car mishap and a police encounter that derails the abduction attempt.
Emily loses sight of the brothers and encounters a group of bullies who steal her bike. At recess, the brothers face the bullies in a grudge match: two on two, with nine points already on the scoreboard. They weather the dirty tactics, rally, and surge to ten straight points, reclaiming Emily’s bike and lifting the mood with teamwork and speed.
Meanwhile, Mori stays sharp, tracking Snyder and his crew to a harbor ship called the Berth 6. That night, Colt learns that Snyder and Mori are old friends, a revelation that deepens the family’s stake in the coming conflict. Fester and his crew attempt another break-in at the house with a fake pizza delivery, subduing the babysitter before the children can react. The brothers suit up in their ninja gis, using household items and clever surroundings to fight back, and—after regrouping with Emily’s help—manage to outsmart the intruders, even spiking their soda with a laxative to buy time.
The tide turns when Snyder’s henchmen abduct the boys to Snyder’s ship, and the shocking truth comes to light: Mori Tanaka is Snyder’s former sensei. The brothers escape in a chaotic scramble, triggering a shipwide alarm while Mori infiltrates the vessel to reach them. Back on deck, Snyder’s challenge to Mori in the ship’s dojo ends in a dramatic duel.
Snyder’s youth and speed initially tilt the odds in his favor, aided by a hidden pepper bomb, until Mori—aweighing experience and quick thinking—gags Snyder with a fistful of Tum-Tum’s jelly beans and turns the fight. Infuriated, Snyder grapples for a gun and tries to shoot Mori and the boys, but Sam arrives with backup and shoots Snyder’s shoulder, bringing the operation to a close. Snyder, Brown, and the remaining henchmen are taken into custody, their plans thwarted.
In the aftermath, Sam reassures his sons that they’ll continue to visit Mori every summer. The family celebration shifts into a quiet night of pizza and togetherness, a reminder of the humor and warmth that still exists beside the danger, even as Mori—who famously hates pizza—joins them at the table for a rare, shared moment of peace.