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.

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.

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.

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.

One Hour Special episode

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.

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.

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.

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.

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

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.

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.

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.

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.

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.

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

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.

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