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.

X, ein von der Mafia beauftragter Killer, versucht einen supersmarten Hacker zu töten, den Mikes Vater beschützt.

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.

Eine Gruppe Diebe, die sich als Vorschulmädchen verkleidet hat, will reich werden, in dem sie eine Druckmaschine für Hundertdollarnoten klaut.

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.

Ein dementer Psychologe lockt die Ninjas in eine Anstalt, um zu testen, ob er die Macht hat, Gut in Böse zu verwandeln.

Im ersten Zweiteiler der Serie versucht der böse Ishina-Clan das Dojo zu finden. Und Mike erfährt, dass er das schwebende Schwert vor den Ishina verteidigen muss.

Note: Nick considers Ishina as a single episode.

Die Ninjas müssen einen Bösewicht namens „Quake“ stoppen. Quake ist ein Riese, der die Stadt mit seine Metallhandschuhen terrorisiert.

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.

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.