Mike Fukanaga is an awkward high school student who discovers that he comes from a long line of ninjas; Mike becomes the leader of a team of crime fighters.

The ninjas pursue a cat burglar who will stop at nothing to get what she wants.

A villain escapes from prison and intentionally gets caught in order to be reunited with his motorcycle gang in another prison.

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.

Owen is having a hard time with the boring discipline of Grandpa's teachings. When he recognizes that an old friend is part of the dangerous Subsiders parkour crew, Owen infiltrates their underground lair to save him. Meanwhile, Mike and Amanda cope with the temporary loss of their partner and friend.

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

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."

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.

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.

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

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.

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!"

One Hour Special episode

Note: Nick considers Ishina as a single episode.

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.

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.

The ninjas end up in detention and discover Jellyface escaped from prison. Now against one another, they try to figure out who's Jellyface before it's too late. Meanwhile, Amanda lies that she got detention to do a report for the school paper, but she really keeps falling asleep in 1st period because of Study Group. (AKA Ninja Training)So Mike suggests they move Study Group to lunch, and Owen and Amanda realize who Jellyface is, because they don't go to the dojo during lunch.

A string of burglaries have occurred and Mike is convinced the Skeleton Crew, an underground secret society with ties to Benjamin Rush High School, is to blame. Yet Amanda and Owen are doubtful of Mike's accusations since he's a staunch believer of urban myths. Owen desperately tries to woo Isabelle, a new Junior transfer, but has no idea she's actually an undercover detective who's also pursing the Skeleton Crew. She also believes that the Supah Ninjas are the ones behind the attacks at Benjamin Rush High School. Mike quotes his grandfather "Things aren't always what they appear to be." When Isabelle goes to the school with backup, they unmask the ninjas, which actually turns out to be the Skeleton Crew (The Supah Ninjas switched masks with them before Isabelle and Martin arrived). The next day, Mike is now Owen's wingman, for a girl named Greta. Mike and Amanda find a note which meant "This isn't over. S.K. (Skeleton King)" meaning the Skeleton Crew may appear in future episodes.

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.

A man named Frostbite (Steve Monroe) starts to capture criminals and do the ninjas' work for them. But Amanda gets suspicious of him when she finds out the police still think they're on the loose. Meanwhile, Amanda tries to help Mike get ready for his date with Julie, telling him about the "hand touch" in which if a girl touches your shoulders she likes you, on your arm, her feelings may change, and on the hand is that she like likes you. While Mike practices what he's gonna say to Julie, she doesn't realize he's actually talking about herself, and once he finishes, she touches his hand and says, "Perfect." After Mike looks down at their hands, Amanda removes her hand, says she has to go, then walks out of the door as quickly as possible. Mike goes on his first date with Julie, with Owen giving him advice through an earpiece.

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.

Mike's cousin, Connor, returns to Empire City to obtain the floating sword and set up a trap to the ninjas. Mike discovers Connor's identity as an Ishina. He also discovers that his grandfather's twin brother Kagema, who has betrayed the Fukanagas and has now returned to lead the Ishina. In a fight with Connor, Mike loses his mon to him, and the episode ends with Connor inserting the mon into the Supah Ninjas' dojo entrance in Mike's bedroom and it opens up in front of him with Mike, Amanda, Owen and Hologramps looking in despair. Meanwhile Mike is upset, thinking that Amanda and Owen have a thing for each other, after Connor tells him they are into each other. Connor tells Owen that Amanda bleaches her hair, and he tells Amanda that Owen likes her.

In the second-season opener, Connor's motives become clear to the trio, who realize they've underestimated how big of a threat he is.

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.

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.

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.

A cheerleader who was once Amanda's rival is released from juvie, and still holds a grudge against her old foe; suspecting that the rival cheerleader will cause problems, Mike and Owen try to catch her doing wrong by posing as cheerleaders.

When Mike forgets about Martin's birthday, he throws him a last minute party to compensate, but when Ishina crash the party, Mike has to find a way to get his dad out of the house while keeping up the birthday party act.

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.

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.

Owen pursues his crush on Paloma Peru; Mike and Amanda bond while filming an audition tape for a game show.

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

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'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.