After the loss of Zane, the Ninja question whether they are still a team. But when they receive a mysterious invitation to take part in the Tournament of Elements, they get a clue that Zane may be well and alive. And our heroes set out to rescue their friend.
When the ninja receive an invitation to partake in the Tournament of Elements and a clue that Zane might be alive, they accept and travel to a Lost Island owned by notorious crime lord Master Chen in order to save their friend.
On the island, Lloyd learns that his father used to train under the deceitful Master Chen and when the Ninja meet the playfully deceitful ruler, they realize they are in a tournament where "only one can remain."
In order to find Zane, the ninja stay in the tournament to get past the first round but Chen complicates things by changing the bracket and pitting Jay against Cole.
Chen pits everyone against each other in a ludicrous roller skating event called Thunderblade. When all contestants team up against the ninja, the ninja share inside information on Chen to get help from a new alliance in order for Lloyd to move on in the tournament.
The ninja have a secret alliance of elemental fighters, Cole has found Zane, and Nya is a spy within Chen's Kabuki to figure out what nefarious plot Chen is up to. But Chen upends the alliance by promising the all-powerful Staff of Elements to the victor, and reveals that he too has a spy in the tournament.
Nya has proof of Chen's plan, but he convinces the contestants to hunt her down with promises to advance the winner, forcing the ninja into a race to get to her first. Lloyd discovers Chen's plan to steal everyone's power so that he can complete a spell and turn his worshipers into Anacondrrai and bring the return of the Serpentine War.
After stealing the remaining contestant's powers, Chen only needs Lloyd's power to complete the spell. Knowing his daughter has feelings for Kai, Chen tries to enlist the Fire Ninja by promising to share secrets about his parents. All the while, Lloyd tries to rescue the ninja, pitting him in a showdown with Chen.
Chen has failed to bring the return of the Serpentine War but Clouse revels that there is another way - his daughter has the ability to absorb the power of every fighter she comes across, so she can complete the ceremony. Skylor finally sees her father for who he truly is and manages to send an SOS to the ninja.
The ninja reunite with Wu and turn to the aid of a shrunken Pythor in order to figure out how to defeat the unstoppable Anacondrai - but before they can get answers, Pythor is abducted by the Anacondrai and Chen uses his essence to make his worshippers' transformation into Anacondrai permanent.
The ninja and fighters discover there's a strategic location called the Corridor of Elders where they can make their last stand against Chen's Anacondrai army... but even with new Destiny Bounty, their forces still aren't strong enough. Fortunately, Pythor escapes Chen's clutches and discovers there is one spell in the Book of Magic that could stop the war, but at a a serious cost.