Role in the film
The ninjas were first seen during TJ Detweiler and his friends attempted escape from Third Street Elementary School (which at the time had been converted into Phillium Benedict's anti-Recess legion's main base of operations for their anti-Recess agenda) after they were forced to reveal themselves due to a combination of both Mikey Blumberg being unable to hold back a particularly loud belch and the ventilation shaft giving way after finding their Weather-Altering Laser shooting at the moon. After everyone minus TJ successfully escaped from the building, the ninjas forced them off the school, with Muriel Finster and Randall Weems (who at the time were themselves doing a failed breakin to the school due to a misunderstanding about TJ and the others breaking in due to Ms. Finster's immense girth getting herself stuck in a ventilation shaft.) witnessing this, giving them a hint that something was deeply wrong at the school.
When the Third Street Elementary School student resistance (led by Gus Griswald) infiltrated the school, an entire unit of the ninjas pursued Spinelli while two units of Secret Service Look-Alike Foot Soldiers pursued Gus Griswold and Vince LaSalle. However, they ended up being chased off by Spinelli's special forces, the Kindergartners, on her orders.
Several more were later dispatched by reinforcements composed of the teacher and staff (led by Ms. Finster), with several being sprayed with grape soda by Gus, as well as manipulated by him into being crushed by Spinelli's flying press (which she had been working on at Wrestling Camp).
Several were smothered and/or arrested in the aftermath of the battle.
- When the ninjas first appear, Gus while fleeing yelled "Ninjas! Why did it have to be ninjas?!", mirroring a line by the titular character in Indiana Jones: Raiders to the Lost Ark when he encountered snakes inside the cavern where the Ark of the Covenant was located inside.