Plot
Every summer, the Douglas brothers, 12-year-old Samuel, 11-year-old Jeffrey, and 6-year-old Michael, visit their grandfather, Mori Tanaka, at his cabin. Mori trains his grandsons in the art of ninjutsu. As the summer comes to an end, Mori bestows on each of them a new "ninja" name based on their personalities: Samuel being 'Rocky', Jeffrey being 'Colt', and Michael being 'Tum-Tum'.
The boys' father, Sam Douglas, is an FBI agent who stages a sting operation to entrap a master criminal named Hugo Snyder in the sale of warheads. Snyder evades the trap with his ninja henchmen, flees by helicopter, and later visits Mori, his former business partner. Mori is tested by Snyder's ninjas and defeats them with his grandsons' help. Face to face, Snyder fails to persuade Mori to train his men and threatens Mori's family if he does not tell Sam, his son-in-law, to cease pursuing him.
When the boys return home, they find their father unenthusiastic about what they learned during their visit and more annoyed by their new names. Emily, a friend of Rocky's, compliments his new name and agrees to ride with them to school the next day.
Snyder develops a plan to kidnap the brothers and use them as leverage against Sam to complete his missile sale. Snyder's consigliere, Nigel Brown, contacts his irresponsible nephew, Fester, a petty criminal surf punk, as well as his buddies, Hammer and Marcus, to kidnap the brothers, but their plans are put on hold due to the FBI's presence. The next day, Fester and his friends follow the brothers to school, but are sidetracked by a fender-bender involving a police car.
Emily becomes separated from the brothers and encounters a group of bullies who steal her bike. At recess, the brothers challenge the bullies to a two-on-two basketball game, giving the bullies a 9-point head start. Despite the bullies' dirty tactics, the brothers score ten consecutive points and win back Emily's bike. Meanwhile, Mori conducts recon on Snyder and his associates, tracking them to a ship, Berth 6, in the harbor.
That night, Colt learns that Snyder and Mori are old friends. Fester and his friends break into the house under the cover of a fake pizza order and subdue the boys' babysitter. Believing it to be a home invasion, the brothers suit up in their ninja gis and masks and fight back using their surroundings and numerous household items. After regrouping in the boys' bedroom, Fester uses Rocky's homemade phone to call Emily over and take her hostage, but the boys outsmart and defeat Fester's group, even spiking their soda with a laxative. After the babysitter is freed, the brothers are overpowered by Snyder's bodyguard, Rushmore, and taken captive aboard Snyder's ship, where they soon learn that their grandfather was Snyder's sensei. The brothers escape, putting the ship on high alert, and manage to subdue Rushmore and many of Snyder's ninjas, while Mori infiltrates the ship to rescue them.
Snyder confronts Mori in the ship dojo and challenges him to a fight for the brothers' freedom. Due to his youth and speed, and a hidden pepper bomb, Snyder gains the upper hand and is prepared to deliver the finishing blow, until Mori gags Snyder with some of Tum-Tum's jelly beans and finally defeats him. Enraged, Snyder grabs a gun from one of his subordinates and attempts to shoot Mori and the boys, but is suddenly shot in the shoulder by Sam, who arrives with his backup to arrest Snyder, Brown, and their henchmen. Sam tells his sons that he will let them continue to visit their grandfather every summer and takes the rest of the night off from work to get pizza with the family, including Mori, who hates pizza.
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