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.
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.
