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.

One Hour Special episode

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.

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.

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.

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

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.

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.

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 gang of thieves go undercover as prep-school girls.

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

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.

Note: Nick considers Ishina as a single episode.

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.

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.

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."

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.

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.

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 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.