The Digital Overlord and the Golden Master

After the defeat of the Overlord, Cyrus Borg rebuilds Ninjago City into a futuristic metropolis called New Ninjago City. The ninja team becomes teachers at Master Wu's Academy. During a field trip to Borg Industries, they meet Pixal, a female android. Cyrus Borg gives the ninja a golden statue with Techno Blades hidden inside. The Overlord reemerges as a computer virus in the Digiverse and takes control of Cyrus Borg and Pixal to create an army of Nindroids using Zane's blueprints.

The Digital Overlord plans to capture Lloyd and use his Golden Power to escape the Digiverse. The ninja team retreat to Lord Garmadon's, now Sensei Garmadon, monastery where they learn The Art of the Silent Fist. Zane releases Pixal from the Overlord's control using Techno Blades. The team splits up after being ambushed by Nindroids. Lloyd and his Father visit Nya's Samurai X cave while the rest of the ninja team infiltrates Ninjago City's power station to cut off the Overlord's power supply, but are forced to fight an army of Nindroids led by General Cryptor, but are able to defeat them. The destruction of the power station causes all nindroids to shut down, including Pixal.

A mysterious hooded figure steals the hard drive containing the Overlord and saves the Digital Overlord by reactivating him with electrocobrai. Wu is captured, transformed into a corrupted cyborg, and sent to Jay's parents' junkyard with the hooded figure by the Digital Overlord, who anticipated the Ninjas' arrival over there. Zane revives Pixal by giving her half of his power source 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 hooded figure and a corrupted Sensei Wu. Wu and the hooded figure are defeated, with the latter leaving behind a white scale. Lloyd and his father head for Hiroshi's Labyrinth to hide from the Overlord's forces.

They decide to go underground to find the Serpentine, who are now led by Skales, to ask him about the white scale. The Serpentine tell them of the legend of the Golden Master, and Skales reveals that only one Serpentine could be the hooded stranger. The Nindroids attack and the ninja must fight to protect the Serpentine. Lloyd is cornered by the Nindroid Mechdragon and the hooded stranger, who reveals himself to be Pythor, having survived the Devourer. Pythor is now white, having been bleached by the venom of the Great Devourer.

Lloyd has been captured by Pythor and is taken away aboard the Mechdragon. The Overlord begins to drain his Golden Power, to regain his physical form and become the Golden Master. Borg tells the ninja they can reboot the system and destroy the Digital Overlord by going into the Digiverse. The Ninja enter the Digiverse, to confront the Overlord but as he grows more powerful, he begins to overwhelm them. In the real world, Pythor, Wu, and the Nindroid army attack Borg Tower, while Garmadon tries to fend them off. The Ninja share Lloyd's golden power and expel the Overlord from the Digiverse. Turning Wu and the corrupted machines in Ninjago City back to normal. Lloyd narrowly escapes as the Mechdragon, as it plummets into the sea, but the Overlord manages to escape the digiverse half-formed.

Pythor and a group of Nindroids free the Overlord from the submerged Mechdragon. Lloyd then gives up his remaining Golden Power at the Temple of Light by restoring the elemental powers of the original four ninja. Wu and Garmadon soon discover that Pythor and the Nindroids have devised a plan known as "Project: Arcturus". Kai is dispatched to follow a Nindroid convoy in the X-1 Prototype, but he is captured after a long chase. The ninja discover a rocket named Arcturus that the Digital Overlord intends to use to retrieve the Golden Weapons from space. The ninja regroup and head to the Lost City of Ouroborus, being told by Garmadon that the Nindroids should be there. After freeing Kai, the ninja make a last-minute decision to board the rocket as it blasts off into space.

The rocket ship heads into the trail of the Arcturus Comet, where the Nindroids seek to recover the remains of the Mega Weapon, which has been blasted into space after its last use. The Ninja attempt to stop them, but are eventually abandoned on the comet's surface, as the Nindroids escape with the gold they sought. The ninja use resources and make a small rocket ship, powered by Zane.

When they are close to Earth, Zane is about to reach critical mass, meaning he will blow, because his "unlimited power" is in fact limited. So the ninja use their elemental shields for the rest of the route to Earth. The Nindroids melt the remains of 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, now grown to a massive size, wreaking havoc on the city. They take refuge in the Temple of Fortitude and devise a plan to shrink the overlord with a pill. The plan fails when Pythor swallows the pill instead, and the Ninjas are subdued. Zane overloads his power source, sacrificing himself to destroy the Golden Master. A memorial service is held for Zane, but however, Zane ultimately survives, trapped in Borg's systems, and rebuilds himself with the help of Pixal.