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.

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.

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

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.

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

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.

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 accidentally brings the mad scientist back to life.

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

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.

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.

Bash is thought to be the ninja.

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 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 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.

Randy and Howard find a note under their 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.

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.

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

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

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

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