Katara Sharp, a seemingly klutzy bookish-type, is actually a knife-throwing cat burglar obsessed with stealing priceless antiquities. While the Ninjas are on to her, she'll stop at nothing to get what she wants.
After learning about the disappearance of an under-cover police detective, the Supah Ninjas discover that the villain Checkmate, a former chess prodigy, is to blame. The Ninjas must now enter into Checkmate's dangerous world.
Owen is having a hard time with the boring discipline side 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.
Amanda's favorite teacher Mr. Bradford, is living a double life. A scientist who used to work for a major pharmaceutical company, Bradford now teaches high school biology but continues to perform controversial tests.
No Face, a former master jewel thief, has been released from jail and is seeking vengeance on those who put him behind bars. Possessing a high tech mask No Face carries out crimes in the guise of others.
Dollhouse, a villain who appears in a white porcelain doll mask turns ordinary people into "living dolls". When Amanda is kidnapped by Dollhouse to be the perfect cheerleader in his doll collection, Owen and Mike must save her.
A group of highly-trained thieves covering as prep school girls have targeted Empire City. The Supah Ninjas, who happen to be on a school field trip, must try to take the girls down while not exposing their ninja personas.
Owen is in a bit of a crime-fighting slump, so Mike and Amanda try to cheer him up by taking him to a concert at the school by their favorite deejay, DJ Elephant Head. But soon they realize DJ Elephant is a dangerous criminal!
Having not been invited to the popular kids' party Owen throws his own party at Mike's house. Amanda's fallen out of favor with the popular crowd, so in order to keep everyone happy she secretly attends both parties.
Dr. Eternum, the demented psychiatrist who runs Eternum Asylum believes he has the power to change human nature and turn good into evil. Eternum lures the ninjas to the asylum in order to test his theory.
The evil Ishina Clan tries to find the dojo in order to defeat the Fukanaga Clan. While trying to defend the dojo, Mike learns it's his destiny to protect the Floating Sword from the Ishina, who won't stop until they possess it.
With Owen and Amanda's advice, Mike finally asks Julie out, only to painfully learn right after that Amanda and Cameron have broken up. Meanwhile, Quake, a gigantic, beast of a man, has been terrorizing Empire City.
Martin and Mike go on a police car ride-along but Mike feels like he's outgrown this family tradition. While out father and son come face to face with Buzzsaw & Optic, half human/half machines, and the kids of evil Mechanov.
Mike, Owen and Amanda are stuck in detention and secrets are unearthed as they figure out who among them is Jelly Face, a person who has escaped prison and assumed the identity of a student to exact revenge at Homecoming.