Martin catches Mike sneaking out of the house and grounds him, and now Mike must find a loophole in Mike's rules that will allow him to help the ninjas stop Evil Grandpa and the Ishina from using their mapping device to locate the dojo.

When Amanda and Mike pair up in the science fair, Owen gets stuck with Quinton as a science fair partner. Quiton does all the work and gets his project stolen from an evil scientist's assistant.

The Ninjas investigate a social media star who uses flash mobs to incite chaos; Paloma grows suspicious of the ninjas.

Amanda McKay starts to develop feelings for Flint Forster, a thief who specializes in the redistribution of wealth, but in trying to keep her crush a secret, her strange behavior leads Owen Reynolds to think she is falling for Mike Fukanaga.

Flint Forster discovers Amanda's true identity and gets a look at her life as a ninja, and when a counterfeiting student takes Amanda and Flint hostage, Mike is forced to save his rival in addition to his friend and ally.

Flint asks Amanda to the Spring Fling; Mike must team up with Flint to rescue Amanda; Amanda must decide if she is going to stay in Empire City or study in Paris.

Mike and the gang are suspicious when unlikley suspects turn bad, including one of Mike's own uncles. Meanwhile, Connor is filming everyone doing embarrassing things for his made-up show, "Conn'd."

A computer geek leads a double life as a super hero named Kickbutt (Lucas Cruikshank), but his alter ego gets in trouble when he steals a mob boss' (Mark Lindsay Chapman) money and uses it to renovate the computer lab at school.

A magician (Vince Corazza) fakes his disappearance, and Owen tries to solve the mystery by reviving his and Mike's magic act, which Mike doesn't favor. Meanwhile, Amanda tries to have a proper date with Cameron, who thinks she has feelings for Owen. And after Mike calls her to give her some info, their date is ruined.

The ninjas take on chess prodigy villain named Checkmate who challenges them in chess-related games putting their lives in danger. Amanda feels she must overachieve at other things after getting her first A-, the worst grade she has ever received in her life.

A biology teacher in school is experimentinting a cure to all diseases with insect DNA. He accidentaly adds too much and turns into a monster. Meanwhile, Mike's annoying cousin Conner stays over for a few days.

A gang of thieves go undercover as prep-school girls.

A demented psychiatrist lures the ninjas to an asylum to test his theory that he has the power to turn good into evil. While investigating, Amanda meets Checkmate again, who in the end of the episode escapes with a message to the Supah Ninjas, "Game On Ninjas!"

Mike goes on a police ride-along with Martin. A villainous brother named Optic (Dennis Keiffer) and his sister Buzzsaw (Danielle Burgio) the duo steal purple diamonds around the city to bring their dying father called Mechanov (Curt Lowens) back to life as a robot.

Limedark (Danny Masterson), a former college actor, kidnaps his former cast mates, who have become famous, and has horrible plans for them. Meanwhile, Owen has trouble hiding his ninja skills and almost exposes his friends and himself twice, once while trying to defend a boy from a shifty-looking senior student who was actually selling cupcakes to raise money for children's hospitals and when Limelight captures his final target. Mike and Amanda scold him afterward but Hologramps takes pity on Owen because he was trying to do the right thing, he also knows how he feels about not receiving enough attention and not getting credit for helping to save Empire City, but he tells him that a ninja's strength comes from within, not the opinion of others.

Tensions flare after Grandfather traps Mike, Owen and Amanda in the dojo to stage an intervention, realizing they've forgotten the true meaning of being Ninjas. Through flashbacks and clips, the Ninjas work out their dilemma of whether or not to go public after Grandfather tells them they've been captured battling a villain on a security camera. After Amanda and Owen want to go public and Mike doesn't, just because it's two against one, they decide to go public. But when they only can have one, Amanda, Mike, and Owen all think that they should be the one. After it is Mike, Grandfather says that not all the tallys have been counted, they do a breathing exercise to reflect on what all has gone on in their ninja lives. Grandfather says that there is no i in ninja to which Amanda keeps complaining about.

Owen Reynolds is excited to enjoy the fame brought on by a viral photo of him in his ninja suit, but before he can come forward, an impostor called the Shadow Master takes credit for the picture, stealing Owen's fifteen minutes of fame.

The Ninjas bring in Kid Q to fix the dojo after it is destroyed and bring Hologramps back, but Kid Q stays longer than the Ninja's had allotted for, and on top of that, he lets Two Ton Harley, their old nemesis, out of prison.

Mike's Cousin Connor returns as a spy and learns that the Kata is the key to finding the floating sword. He tries to retrieve it, but Mike defeats him and takes the sword. At the dojo, Quinton manages to fix Grandpa. In the last scene, Owen realizes that Amanda likes Mike. Mike goes to his locker and finds his grandpa's brother, who captures Mike; ending the series with Kagema flying off with Mike.

A masked eco-terrorist seeks revenge. Amanda falls for a rich boy who could be the ninjas new enemy.

When Amanda is kidnapped by a villain who turns people into living dolls, Owen and Mike must infiltrate the villain's lair to rescue her.

The ninjas must stop a mysterious assassin hired by the mob to kill a star witness being protected by Martin.

Mike and Amanda try to cheer up Owen by taking him to a concert at the school.

Amanda struggles with popularity after she isn't invited to Melanie's party, but she soon gets invited thanks to Kelly; however, Owen is throwing a party on the same night, so Amanda attends both. Meanwhile, the ninjas fight a villain known as Snakeskin who is really their attractive guidance counselor, Ms. Scott (Amy Lucas), who is stealing Devil Diamond Snakes and plans to use their venom as revenge on the popular kids at Melanie's party. With all the kids locked in with a canister of the venom, it's up to Amanda to save them.

The ninjas must stop a villain named "Quake" (Esteban Cueto), a large man with metal gloves that is terrorizing the city. Amanda starts to have feelings for Mike. During training when they are balancing on a piece of wood, Mike is asking Amanda if he should ask a girl out. Amanda has a big grin on her face because she thinks it is her, but when she says, "Yeah, go for it," Mike says, "That's great. I'll ask Julie tonight." Then she says, "Julie?" in a depressed voice and falls off the wood because she lost her balance thinking of the thought. Mike looks concerned when Amanda falls off. Amanda says, "I'm okay, everything's fine," then sits up with a hurt expression directed at Mike. Through the rest of the episodes, amanda constantly shows signs of jealous about Mike and Julie. Owen encourages Mike to ask out Julie, he then finds out that Amanda has broken up with Cameron.