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.

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.

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

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

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.