Sibling blacksmiths Kai and Nya meet a mysterious old man Master Wu, who seeks their help to train under him against the threat of his soon to return brother Garmadon and his new army of Skulkin who dominate the Underworld under leadership of former king Samukai, whom Garmadon overthrew. After Nya is abducted, Kai joins Wu's three other students, Jay, Zane, and Cole to find and protect the Golden Weapons of Spinjitzu. Note: This episode was released in some regions as a 22-minute episode along with "The Golden Weapon".
Garmadon's ultimate weapon, the Garmatron (Which in effect is a giant Cannon), is completed. The Overlord, the Stone Army, and Garmadon drive the vehicle to the coast of the Dark Island, but not before testing it out on Nya. The Ninja pursue Garmadon to the coast, and discover that Nya has turned evil, gaining all of Garmadon's dark abilities in the process. Kai, Jay, Zane, and Cole stay behind to deal with Nya, while Lloyd, Misako, and Sensei Wu rush to stop the Garmatron. They fail, and Garmadon turns Jamonkai Village, and the town around Four Weapons evil. The shift in the balance of good and evil allows the Overlord to poccess Garmadon's body and begin to transform into his original form. Lloyd challenges him, but is injured in the resulting battle.
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 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.
When Morro gives chase to the Bounty and steals Wu's staff, Wu shares the story of Morro: the boy who wanted to be the Green Ninja - and the Ninja discover Wu's staff contained 3 symbols that lead to the Tomb of the First Spinjitzu Master which holds a mysterious relic that could alter the course of Ninjago.
The Ninja travel to the Village of Stiix to find the thief who stole the scroll of Airjitzu, but the self-serving Ronin isn't keen to sell it cheaply so the Ninja must figure out a way to make money on the docks - and when they fail to make enough cash, the Ninja decide to steal it - but have a run in with Morro and Soul Archer.
The Ninja hear of another way to learn Airjitzu - from the ghost of Sensei Yang at his haunted temple - but there's a warning; if you are trapped in it by sunrise, you will become a ghost, too. Meanwhile, doubting she's a Water Ninja, Nya quits her training to take Ronan to her Samurai X cave...but has a run in with Moro.
Now that the Ninja know Airjitzu, they get briefed about how the next stage to finding the tomb is to get 'The Sword of Sanctuary' from Cloud Kingdom, which can only be reached from the top of the Wailing Alps. The Ninja go on the treacherous mission up the tallest peak in blizzard conditions using their mechs, but Cole struggles with his ghostly form.
In Cloud Kingdom, a realm where destinies are written, the Ninja must get the Sword of Sanctuary, a powerful relic that can see past the traps surrounding the tomb of the First Spinjitzu Master - but tensions are high as Moro's escape from the Cursed Realm has put the future in chaos, and they won't give the Sword to the Ninja unless the Master Writer meets them personally.
As the ghosts converge around and mobilize the Preeminent into a hulking giant behemoth, the Ninja use Airjitzu to fight the mobile beast in an attempt to slow it down — while, at the same time, Lloyd faces off with Moro, battling over the Realm Crystal; a fight that takes them in and out of different realms.
The Ninja are taken to the Dragon Hunter’s village. Planning to escape, they resolve to build a simulated Firstbourne with Cole and Wu. The resistance, led by a newly motivated Lloyd devise tactics for overthrowing Garmadon. Dareth, feeling excluded due to his lack of elemental power, convinces Mistaké to help him help obtain ‘brown power’.