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.

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 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.

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.

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.

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.

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

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

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.

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.

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

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.

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 helps students escape from Detention Island.

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 accidentally brings the mad scientist back to life.

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