They witness a confrontation between their grandfather and Hugo Snyder, ex-student/partner of Tanaka and a criminal who is being pursued by the boys' father, FBI agent Sam Douglas.
Snyder plans to kidnap the boys with the help of his assistant Mr. Brown, who employs his irresponsible nephew Fester, and his friends Hammer and Marcus to abduct them.
Meanwhile, the boys escape their containment cell using the training bestowed upon them by their Grandfather and begin fighting their way out of the ship, leading up to a final confrontation between Snyder and Mori.
During their Japanese adventure, the kids learn important skills and life lessons which help them win the final baseball game of their season, with Colt hitting a home run.
A poor sport on the opposing team picks on them; Darren attempts to attack Miyo but ends up getting knocked unconscious during one of the final scenes.