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 rev... Read more

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... Read more

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 ... Read more

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 t... Read more

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 Lime... Read more

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, a... Read more

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 doe... Read more

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 ... Read more