Randy Cunningham, a 9th grade kid, becomes a ninja and is to protect Norisville High School.

Randy and Howard become judges for their school's talent show and Randy tells Howard that he should be "the mean judge." But the Sorcerer takes this chance and makes all the failing acts monsters.

Howard accidentally tells everyone on a web show that he knows who the ninja is and he is captured by McFist, who demands that he tell him who the ninja is.

The Ninja fights a lizard, which copies a sample of his snot. Later Randy and Howard attend a party Bash is throwing, but it's a scheme so McFist can find the ninja by sampling everyone's snot bombs and matching it to the ninja.

Randy and Howard want to win the Science Fair, but will they go too far?

Randy and Howard find a note under their school.

A Mexican death bear threatens the school.

Randy must find a way to juggle his life as a ninja and his friendship with Howard during the battle of the bands, while McFist tries to use a truth device that will reveal the ninja's identity during the show.

After a fight between Randy and Howard, a monster attacks during the school's annual routine "monster drill" where Howard is pretending to be the ninja. Randy must find a way to get to his mask and to apologize to his friend.

Randy Cunningham looks for the Skunk Pine in order to restock his smoke bombs. When Randy finds the Skunk Pine, it is stolen by Hannibal McFist to use as a Christmas tree party at McFist Industries. Randy also discovers that Howard is at Hannibal McFist's Christmas party when his father's company was bought by McFist Industries. When Randy infiltrates the Christmas party as a Ninja Santa Claus, he ends up fighting a robotic snowman and an army of robotic Christmas Elves in order to restock his smoke bombs.

Franz Nukid, a strange new exchange student, threatens to destroy the Ninja as well as Randy and Howard's friendship which Hannibal McFist takes advantage of.

When Randy and Howard are forced to share a lunch table with the outcast group "Der Monster Klub", Randy accidentally tells them how to get people stank'd, and they realize these oddballs are playing a dangerous game that could destroy the whole school even when the Sorcerer gets involved when some of the members get depressed.

Randy helps students escape from Detention Island.

Bash is thought to be the ninja.

Randy and Howard seek revenge on a French exchange student who stole their Internet video fame - only to cause him to stank out and create a scene they weren't expecting.

When Randy loses the NinjaNomicon, he must save it before hundreds of years of Ninja wisdom is revealed to his enemies.

Randy and Howard are eager to ride a new roller coaster but first, the Ninja must stop a Robo-Ape uprising.

The Ninja accidentally summons a giant monster when he uses an ancient ninja lesson during a rap battle.

Randy must go with Howard to CluckFest under the threat of Bash Johnson. This won't be easy for Randy since he is afraid of chickens. Meanwhile, Hannibal McFist and Willem Viceroy III unleash a fear-pooping robotic rhinoceros called the Rhinosaurus that forces everyone to confront their worst fear as part of their plot to find the Ninja's greatest fear and take advantage of it.

Randy and Howard must sacrifice everything to prevent the Ninja's ultimate enemy from running amuck.

When Randy inadvertently mind-wipes himself and develops amnesia, Howard must fill in as the Ninja until Randy can get his memory back.

Mac Antfee (voiced by David Koechner) returns to Norrisville as a motivational speaker, only to have Randy reignite his burning desire to destroy the Ninja and take his place.

Randy, Howard, and all the boys at Norrisville High are entranced by the new girl in school named Amanda Levay. Little do they know that she's the Sorceress (voiced by Jennifer Tilly), the Sorcerer's long lost love in disguise where she has plans to free the Sorcerer.

Coach Green brings back an old Norrisville High tradition, Prank Day.

During "Ninja Day" McFist schemes to steal the spotlight by introducing a new hero - Himself.