They are voiced by Jack Angel.
Taking Over Third Street Elementary
The ninjas were hired by the Legion following Benedict's dismissal as Secretary of Education due to his attempt of abolishing recess throughout the country. Sharing Benedict's belief of abolishing recess to raise test scores, the ninjas, along with the Anti-Recess Agents, became involved in Benedict's next plot to get rid of summer vacation. To do so, they helped breaking into a U.S. military base, where they stole a tractor beam. They would later take over Third Street Elementary during the summer, as Benedict used to be principal until his firing in 1968 due to his anti-recess policy. With the school closed for the summer, the Legion used the school as a base for their own operations, even the agents are acting out as guards in case anybody would investigate the situation.
As it turns out, Benedict plans to use the tractor beam to move the Moon at lunar perigee (the time when the Moon is closest to the Earth) to create permanent winter throughout the world so that student will have to stay in school, in hopes that it would raise test scores. Upon hearing that T.J. Detweiller and his friends have broken into the school to find out what's going on, Benedict sent the ninjas to capture them, causing T.J. to be captured alongside Principal Prickly while his friends escape.
Fighting Against the Students and Staff
With Prickly and T.J. in danger, T.J.'s friends gathered up all the students from their summer camps to help fight back against the Legion; even the groundskeeper Ms. Finster brought up the teachers and staff to help the students fight back against the Legion. As such, the students laid down traps on the agents and ninjas, even the kindergarteners end up scaring the ninjas away when they were chasing Spinelli.
Unperturbed, Benedict orders both the agents and ninjas to finish off the students and staff, though their efforts became for naught when Vince throws a baseball at the tractor beam, destroying it and foiling Benedict's plot. The ninjas were arrested and sent to prison along with Benedict and his other men for their crimes.