Snyder ends up having his henchmen kidnap Rocky, Colt, and Tum Tum from their home and bring them to his freighter, and he has a note left behind for their FBI agent father Sam warning him to not interfere with an upcoming weapons deal he is doing on the freighter or else he will kill the boys. Mori shows up after Sam and his wife see the note, having feared for the family’s safety, and convinces Sam to hold off on doing an assault on the freighter and give him one hour to sneak onto it and save the boys himself.
The boys get free of their confines and fight their way through Snyder’s henchmen, ultimately reuniting with Mori in the training room. However, Snyder’s ninjas then surround them and Snyder himself appears. Mori challenges him to a fight, with the stakes being that, if he loses, he will die, but if he wins, then the boys are allowed to go free. Mori more or less defeats Snyder after he gags him with jelly beans that Tum Tum had given him before the fight “for luck.” Snyder is unwilling to accept the loss, however, and he grabs a gun to shoot them with, but Sam arrives with a legion of SWAT officers and shoots him in the shoulder to stop him.
Snyder and his men are arrested, Sam gives the boys his blessing to continue training with Mori, and then the whole family goes out for pizza to celebrate.
After Fester (Patrick Labyorteaux) and his friends get beat up by Rocky (Michael Treanor), Colt (Max Elliott Slade), and Tum Tum (Chad Power) at their home when they try to kidnap them for Snyder (Rand Kingsley), Snyder’s bodyguard Rushmore (Professor Toru Tanaka), his assistant Mr. Brown (Joel Swetow), and some of his ninja goons come into the house and complete the task for them. The boys’ friend Emily (Kate Sargeant) whom Fester lured over to the house and tried to use as a hostage in an attempt to make the boys surrender is given a note by them to give to the boys’ parents Sam (Alan McRae) and Jessica (Margarita Franco), which states that Snyder has the kids on his freighter in the harbor, and if Sam interferes with the upcoming weapons deal he is conducting there, he will have the boys killed.
Emily calls the cops, and after Sam and Jessica show up, Emily hands them the note. Mori (Victor Wong) then appears, having feared for the family’s safety, and Jessica informs him about what has become of his grandsons. He convinces Sam to hold off on doing any kind of assault on the freighter with his fellow FBI agents and give him one hour to save them, because he knows that he can get onto the freighter unseen and thus not cause any alarm, plus Snyder believes himself to be a ninja, so it will take a ninja to break him.
The brothers manage to get free of their confines just as Mori sneaks on board the ship, and they fight several of Snyder’s ninjas all the way to the training room, where they come face to face with Rushmore. Mori shows up high above and tells the boys to hit his pressure points like on the practice dummy they trained with earlier, and they apply this knowledge and put Rushmore down for the count. As the ninjas present aim their guns at the boys, Mori jumps down to them, but they then find themselves surrounded by more ninjas. Snyder then shows up, and Mori soon challenges him to a fight, with the stakes being that, if he loses, he will die, but if he wins, then the boys are allowed to go free. Before the fight begins, Mori talks with his grandsons, and Tum Tum gives him some jelly beans “for luck.”
Snyder proves to be the better fighter due to his youth (plus he uses a pepper bomb on Mori to temporarily blind him), but when he attempts to finish off Mori, Mori takes the jelly beans and drops them down his throat to make him gag, thus giving him the opening to turn the tide and more or less defeat Snyder. The boys rush up to Mori and hug him, but Snyder unwilling to accept defeat grabs a gun and prepares to shoot them all. Suddenly, he gets a bullet shot into his shoulder, and we see Sam high above them along with a legion of FBI officers.
Snyder and his men are taken into custody, and Sam later tells the boys that they are the real heroes here tonight, and he gives them his permission to continue to see Mori and train with him. He then takes them, Mori, and Jessica out for pizza to celebrate. As they go, Rocky narrates that, from that moment on, he knew that he and his brothers had truly become ninjas.