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.

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 a robot disguised as a rival school's chess team member crushes Norrisville High's record - and their spirit, a mass stanking breaks out.

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.

A feud breaks out when Howard is accepted into a school club and Randy isn't. But when Howard is in danger, the Ninja must put aside his grudge and come to the rescue.

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

Randy must stop a former Norrisville Ninja-turned-nemesis from recruiting an army intended to destroy the Ninja.

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.

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.

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

When Randy and Howard don’t have enough money to buy a McSatchle, they get jobs at McFist-O-Plex and Howard becomes Randy’s manager.

When Randy helps Hannibal McFist’s hippie brother Terry (voiced by Steve Zahn) take control of McFist Industries, Whoopee World is turned into a fart-powered nightmare.

In order to score a limousine ride with soccer super star Pitch Kickham (voiced by Simon Pegg), the Ninja swipes a pair of shorts to help him win a shoot-out competition. When McFist sends an I.D. Bot to find the shorts, Randy's identity is compromised and Howard must take Randy's place in the competition.

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.

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.

When Randy lies that his name is Ranginald Bagel (voiced by Gilbert Gottfried), he puts the real Ranginald Bagel in danger of McFist's fury.

Due to their ability to break McFist products, the boys become product testers at McFist Industries and inadvertently help Viceroy an indestructible ninja-seeking robot.

Randy and Howard follow Theresa Fowler (voiced by Sarah Hyland) and the rest of their classmates to a cool new club downtown only to discover that the Sorceress (voiced by Jennifer Tilly) has returned to seek revenge on the Ninja.

During the 50th Anniversary Celebration of McFist Industries, the Ninja outs McFist as a villain to the entire town. But with his cover blown, McFist is finally able to focus all of his power on destroying the Ninja.

Randy becomes so dependent on the Nomicon’s wisdom that he goes to it for advice on everything. To teach him a lesson, the Nomicon traps him inside and puts an alternate consciousness in Randy’s body, forcing Randy to try to find a way out of this mess.

Randy and Howard accidentally stumble back in time and accidentally stop the original Ninja from stopping the Sorcerer.

Randy and Howard must work the the original Ninja defeat the Sorcerer in order to have a present to return to.