Following the events of the Overlord's defeat, much has changed: Ninjago City is now a futuristic metropolis and renamed New Ninjago City, the ninja, Sensei Wu, Nya and Dareth are teachers at Darkley's (now Sensei Wu's Academy) and Lloyd travels around Ninjago celebrating his victory. However, everyone is recalled up into action when the Overlord is revealed to have survived in the Digiverse and takes over all technology. Cyrus Borg gives the ninja the Techno-Blades and new suits. Sensei Wu is captured. Towards the end of the episode, P.I.X.A.L. is shown to be producing Nindroids. 

The ninja, pursued by Nindroids, retreat to Lord Garmadon's monastery. While Zane is guarding the Techno-Blades, he captures P.I.X.A.L., who was attempting their theft. After hacking her, the team is ambushed by Nindroids. After escaping the ambush, Lloyd and Garmadon visit Nya's Samurai X cave, while the ninja head to Ninjago City's power station, infiltrating the city using a circus train. Once inside, they are met with the Min-Droid. The ninja manage to use the Nindroids' lasers to destroy the power station, but this comes at the momentary loss of P.I.X.A.L., with her last words at the time being "we are compatible?" to Zane, who was by her side and responded yes. 

The Overlord's code is saved by a mysterious hooded figure who claims to be an ally. Meanwhile, Zane gives half of his power source to revive P.I.X.A.L., while the Ninja search for a way to return to New Ninjago City and eventually reach Jay's parents' junkyard. There, they are attacked by the mysterious hooded figure and Sensei Wu, who has been turned evil. Jay turns on Cole after discovering what has been going on between him and Nya. Wu and the hooded figure are defeated, but the figure leaves behind a white scale as a clue for identification. In the meantime, Lloyd and his father head for Hiroshi's Labyrinth planning to stay hidden from the Overlord's forces. 

The ninja journey under Ninjago City to visit the Serpentine, believing the white scale belongs to one of them. Instead, they find out that the Serpentine became a civilized race and are told the legend of the Curse of the Golden Master. Eventually, an army of Nindroids attacks the Serpentine, and the ninja protect them. In the meantime, Lloyd and his father encounter an army of Nindroids in Hiroshi's Labyrinth. Lloyd tries to escape, but is cornered by the Nindroid Mechdragon and ambushed by the hooded stranger, who reveals himself to be Pythor, having survived the Devourer. Lloyd is taken aboard the Mechdragon and flown off. 

The ninja enter the Digiverse, the digital reality, where they make their stand against the Overlord. Pythor, Wu, and an army of Nindroids attack Borg Tower. Garmadon arrives, battling his brother while Borg is kidnapped by the Nindroids. In the Digiverse, the ninja confront the Digital Overlord, but they are being swiftly overwhelmed, as he gains more of Lloyd's golden power from the outside world. Zane leads the Ninja to strike back at the Overlord, sharing Lloyd's golden power to get the Overlord out of the Digiverse. After they succeed, Wu and all the other corrupted machines in Ninjago City turn back to normal. Lloyd.

After Pythor and a group of Nindroids free the Overlord from the submerged Mechdragon, Wu and Garmadon discover that Pythor and the Nindroids have a plan known as "Project: Arcturus". P.I.X.A.L. dispatches Kai to follow a group of Nindroid convoys in the X-1 Charger. After a lengthy chase, Kai is captured by Pythor and the Nindroids. The ninja regroup and head to the Lost City of Ouroborus, where they discover an underground rocket ship - Arcturus. After freeing Kai and battling several Nindroids, the ninja make a last-minute decision to board the rocket ship. 

While on board the Arcturus rocket ship, the ninja obtain space suits and battle a group of Nindroids on top of the ship. Arcturus heads into the trail of a comet, where the fused molding of the Golden Weapons is located. The Nindroids obtain the dangerous object, with the ninja going in pursuit of them. A chase breaks out on the comet, with the ninja eventually being abandoned there by the Nindroids, who escape with the fused Golden Weapons. 

The Nindroids melt the Golden Weapons into a suit of armor for the Overlord, who has transformed into the Golden Master. The ninja return to Ninjago from space to find the Golden Master wreaking havoc on the city. Using the Temple of Fortitude, the ninja gain a means of hiding from the Golden Master, before attempting to shrink him using a pill, which Pythor swallows. As his allies are subdued, Zane sacrifices himself to save the others, killing himself and the Golden Master. In the end, a remembrance ceremony is held for Zane, and in Borg's tower, P.I.X.A.L. finds out that he may still be alive.