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

Randy and Howard try to get into a cool zone in the bleachers when watching their school play basketball. When one of the triangle-playing band members is fired, The Sorcerer turns him into a ferocious monster.

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.

When Randy discovers that the Norrisville philanthropist, Hannibal McFist, is his enemy, he has a hard time trying to convince Howard that the one they believed to be their hero is actually an evil villain working with the Sorcerer.

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 takes a trip to the town's volcano, but it's probably not going to be a nice stop-by.

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

Randy and Howard find a note under their school.

Randy accidentally brings the mad scientist back to life.

Randy and Howard wonder why everyone in town is turning into zombies.

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.

After a power outage at school, a Stankified Monster frozen in ice is freed. When Randy de-stanks him, he and Howard learn that his name is Dickie and his monster form was frozen in ice by the Ninja of 1985. When Dickie (voiced by Bobcat Goldthwait) is saddened by this and how he missed his chance with Tawny (voiced by Annie Potts), The Sorcerer takes the opportunity to re-stank him and find out what is the object of his stank.

The Wave Slayer relays are occurring in Norrisville as Randy and Howard accidentally wrecks the Wave Slayer where an accident injures Buttermaker and causes Howard to take his place. The Sorcerer takes the opportunity to Stankify Buttermaker (voiced by Sterling Knight) into an aquatic monster that attacks the opposing team.

Randy must learn a valuable new lesson about respect and humility when after accidentally breaking his sword. He enlists the help of the blind metal shop teacher S. Ward Smith (voiced by John Witherspoon) to get a custom-made sword. Meanwhile, S. Ward Smith's protege Brent believes he was replaced by Howard and the Sorcerer to Stankify Brent (voiced by Jason Earles) into a monster that goes after Howard.

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's video game battle gets out of hand, the Ninja must save the town from a giant robot.

School Spirit Week turns into a disaster after Howard is possessed by a mythical demon bird called the Tengu which Randy releases.

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.

During the premiere a new 6D film, the movie's title character comes to life and threatens to destroy Norrisville.

Randy helps students escape from Detention Island.

Bash is thought to be the ninja.