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

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.

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

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.

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.

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.

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.

During Ninja Day, McFist schemes to steal the spotlight by introducing a new hero - himself; the real Ranginald is in danger of McFist's fury.

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 misuses his Ninja powers, and the Nomicon refuses to let him Ninja out and rescue Howard from a psychotic Cajun trapper named Catfish Booray.

The McFreak Show arrives in town and Randy is convinced that he wants a McFreak as a pet. But when the McFreaks go on a rampage, he realizes that wild animals don't really make the best pets.

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