A solitary wanderer meets Kai, a young sword-maker, and his sister Nia in their small farming village right before a terrifying skeleton army arrives, ransacking their shop. The army takes a map hidden by their father years ago and Nia! The wanderer turns out to be Sensei Wu, an old friend of their father's. He promises to help Kai find his sister, but first Kai must become a ninja and master the art of spinjitzu. Kai begins his training and soon meets Sensei Wu's other ninja's, who realize they've all been recruited for very specific skill sets.

Long ago, four weapons of spinjitzu were created by a great warrior. When he passed, his sons were tasked with protecting them. However, the older brother, Lord Garmadon, wanted to use the weapons for his own powerful and evil intents. Sensei Wu was forced to banish his brother to the Underworld and hide the four weapons with dragons as guardians. However, Lord Garmadon has recruited an army of skeletons to find the map that will lead them to the four weapons. Sensei Wu needs Kai, Zane, Cole and Jay to use spinjitzu and the Tornado of Creation to find the weapons first. Only then will the world be safe.

The four Ninja are snapped out of their post-hero complacency when Lord Garmadon's young son Lloyd shows up and tries to pick up where his father left off. The Ninja dismiss him as a threat, but regret that choice after Lloyd wakes up the evil snake tribe. A prophecy is revealed that states a green ninja will ultimately defeat Lord Garmadon.

Back in training mode with the looming threat of Lloyd and the Hypnobrai, Zane wanders after a Falcon and lands himself in a heap of trouble. The rest of the Ninja leave the training dojo to help him and return to find that the snakes have burned it to the ground.

Lloyd, having been kicked out of the Hynobrai snake tribe unlocks a second tribe – The Fangpyres – to help him regain control. The Ninja are busy setting up their new HQ that Zane discovered, but are called to duty when the Fangpyres attack the village where Jay's family lives.

After the Fangpyres join forces with the Hypnobrai, Lloyd awakens Pythor – the last remaining snake of the Anacondrai tribe. Pythor lures Lloyd under his spell and steals a map from him that will show him where the remaining two snakes tribes dwell and Uncle Sensei saves Lloyd from doom.