The Nindroid Conflict was an event that took place after the final battle and shortly before the Tournament of Elements. It was fought with the Ninja and their allies, including Garmadon, Wu, Nya, P.I.X.A.L. and Cyrus Borg, who went up against the Overlord, Pythor, and an army of corrupted Nindroids. The Overlord sought to become an ancient being, the Golden Master, by stealing Lloyd's Golden Power and melting the Golden Weapons into a dangerous mech.
After the Overlord was defeated by Lloyd, his spirit unknowningly survived in the form of a computer virus. The Overlord possessed Cyrus Borg and seized control of Borg Industries' various machines, as well as the Nindroids, turning them against the people of Ninjago and bringing the Ninja into a new conflict. The Overlord seeks to steal Lloyd's Golden Power to make himself a new body.
The Ninja go to Wind Farms Power Station, where they shut down the city's power in an effort to defeat the Nindroids while Garmadon and Lloyd get as far away from society as possible to evade the Overlord. As the two travel across Ninjago, Pythor allies with the Overlord and revives the Nindroids using Electrocobrai, allowing them to function on their own. The Ninja meet with the Serpentine, who tell them about the curse of the Golden Master before the Nindroids invade their home and attack them. After the Ninja defeat the Nindroids, Garmadon and Lloyd are found by their adversaries in Hiroshi's Labyrinth. Pythor uses the Nindroid MechDragon to capture Lloyd and take him back to Ninjago.
Pythor immediately begins draining Lloyd of his Golden Power to transform the Overlord into the Golden Master. The Ninja go to the Digiverse to destroy the Overlord virus, while Pythor, several Nindroids and a corrupted Wu break into Borg Tower to stop them. While the Ninja succeed in destroying the virus, the transference of the Golden Power is completed, and Lloyd narrowly escapes as the MechDragon crashes. Pythor, Cryptor and the Nindroids rescue the Overlord's new body from the MechDragon before setting up a new base at the Lost City of Ouroboros. Seeking to obtain the Golden Weapons, they construct a rocket that will take them to Arcturus, where the remains of the weapons lie. The Nindroids travel into space with the Ninja stowing away on their ship. They manage to find the remains of the Golden Weapons and take them back to Ninjago City, creating a powerful mech for the Golden Master while the Ninja are left on Arcturus.
As the Golden Master is born, he begins wreaking havoc on Ninjago City, while the Ninja build their own spaceship to escape Arcturus and return to Ninjago. After successfully doing so, they make their way into the city, which is being ravaged by the Golden Master. Despite losing their vehicles, the Ninja escape the Golden Master and take refuge in the Temple of Fortitude, which protects them from the Golden Power. The Ninja wear Stone Armor to repel the Golden Power, allowing them to run through the city and confront the Golden Master at Borg Tower. During this time, the Serpentine return to the surface, helping the people of Ninjago City to retreat underground and evade the ensuing chaos.
Wu and Garmadon make an unsuccessful attempt to shrink the Golden Master, instead shrinking Pythor, and the Golden Master incapacitates all the Ninja except Zane. At that moment, Zane confronts the Golden Master himself, freezing him and destroying both of their bodies in the process. The Overlord survives the ordeal, though his spirit is dormant, while Zane is thought dead, and a funeral was held for him days later. However, Zane actually survived, having built himself a new body before being captured by Ronin and sold to Master Chen. As a result of this, the Ninja would be lured into the Tournament of Elements, which would soon give way to the Second Serpentine War.