The Ninja team breaks up and goes their separate ways after the loss of Zane. Lloyd reunites them. Shortly after reuniting, however, they receive a message that Zane is alive and the Ninja must compete in evil Master Chen's Tournament of Elements if they wish to see him again. Sensei Garmadon accompanies them onto Chen's ship, where they discover they aren't the only ones with elemental powers, as there are other descendants of elemental masters such as speed, nature, gravity, mind etc.

After the ninja arrive at Chen's island, Garmadon tells them he used to train under Chen. When inside, Chen himself greets the Elemental Masters, and tells them about the Tournament of Elements and the Jade Blades. In the end, Karlof becomes the first Elemental Master to lose. While the ninja are searching for Zane, they accidentally stumble into a secret gathering of Chen and his cultists just in time to see Chen steal Karlof's powers.

Zane has lost his memory, but regains it after meeting P.I.X.A.L. in another room. He discovers P.I.X.A.L. has been scraped but Zane puts her hard-drive inside himself, becoming compatible with her. However, Clouse catches and tasers him. Meanwhile, Gravis has to fight Griffin, Bolobo has to fight Neuro, and Kai has to fight Ash. The winners Griffin, Neuro, and Kai advance in the tournament. Clouse gets revenge on the Ninja by having Jay and Cole fight each other. The Ninja try to get help from Neuro, but he fails to break into Chen's quarters. Cole and Jay fight each other and eventually, Cole gives up the Jade Blade to Jay, saying, "She's yours, Jay," and gets knocked out of the tournament. This ends their long rivalry over Nya for good. 

After Jacob loses to Skylor, he is brought to Chen's underground factory, where Cole, now powerless, tries to find a way of escaping. Clouse catches Jacob trying to escape and makes him an example and feeding him to his serpent, the second-largest snake in Ninjago. Cole sees Zane locked up and promises to release him. Nya uses her new vehicle to locate and follow the Ninja on Chen's island, but Dareth ends up coming along as well. Meanwhile, Master Chen stages an event called "Thunderblade" (In which two contestants wear roller skates and attempt to make as many laps as possible while carrying a Jade Blade, and the others can help either side) as a contest between Lloyd and Camille, Master of Form.

The Ninja form an alliance with the Elemental Masters after convincing them of Chen's true plan. Chen responds by spreading the rumor that he has a spy within and the Elemental Masters interrogate each other with no results, weakening the alliance. Meanwhile, Nya enters Chen's palace, disguised as a Kabuki, and steals Clouse's spell (a transformation spell on pg. 139) which is revealed to turn Chen's followers into Anacondrai. Cole and Zane manage to break out of Chen's factory.

After Nya stole Clouse's spell, Chen states that whoever finds Nya wins the tournament altogether. Lloyd learns how to create a dragon without his Golden Power and, along with his father, stumbles upon the place where a great battle between the Elemental Masters and the Anacondrai took place, and Garmadon tells Lloyd the story of how Master Chen convinced both sides to declare war. In the war's aftermath, the Anacondrai Generals were banished to the Cursed Realm while the remaining Serpentine were locked in tombs. Meanwhile, Chen reveals his true goals, capturing all the Elemental Masters except for Lloyd (Lloyd did not take any "gift" from Chen). Skylor is also revealed to be Chen's spy and daughter. 

Master Chen drains all the Elemental Masters' powers except Lloyd's. Cole, Zane, and Karlof lead the imprisoned Elemental Masters into escaping the factory. Chen has Kai betray Lloyd and trick him into battling, where Chen uses all the other Elemental Powers on Lloyd and wins, obtaining the Ninja's element. However, Kai and Skylor take Chen's staff and destroy it, releasing the powers back to the Elemental Masters.

Although all the Masters have escaped, Clouse discovers that Skylor's Amber can still be used to gain all the Elemental Powers. Skylor and Kai attempt to escape, but are captured. Clouse battles Garmadon and tries to banish him to the Cursed Realm, but Lord Garmadon escapes and Clouse gets banished instead. Chen manages to complete Clouse's spell without him, turning himself, his followers, and everyone who has the Anacondrai symbol on their back (even Skylor and Garmadon but both of them never turn out to be evil) into Anacondrai. Then, he sends his army by air back to Ninjago. Meanwhile, Kai and Skylor escape.

With Chen's Anacondrai army on the loose, the Ninja visit Kryptarium Prison, where they meet shrunken Pythor and ask for his assistance. Coincidentally, Master Chen has learned the spell has temporary effects and only an essence of a true Anacondrai can make it permanent and goes to the prison to capture Pythor. Then, he sends all of his army with trucks at various locations, and the Elemental Masters follow them, but it turns out to be a huge trap, as Chen is already attacking Ninjago with his full force.

The Elemental Masters discover there's a strategic location called the Corridor of Elders where they can make their last stand against Chen's Anacondrai army. Pythor escapes Chen's clutches and discovers there is a spell in Clouse's spellbook that could stop the war, but at a serious cost. Garmadon banishes himself to the Cursed Realm in order to release the spirits of the Anacondrai Generals, who banish Chen and his army as well. Skylor, who's no longer an Anacondrai, decides to run her father's noodle business. The Ninja burn the Spellbook and pay tribute to Garmadon. They build Garmadon's statue on the Corridor Of Elders.