The Golden Ninja

Without the Golden Weapons, the ninja have lost their elemental powers. They decide to get jobs to rent an apartment but working overtime to afford the rent leaves them with no time to train Lloyd. Meanwhile, Lord Garmadon rebuilds the Destiny's Bounty, and persuades the Serpentine to follow him. The Serpentine Generals refuse to join and plot to kidnap Lloyd instead. They distract the Ninja, who are busy with their work, while Skales sneaks into to the Ninjas' apartment, but he is captured and arrested. Lord Garmadon and the Serpentine fly to the Golden Peaks and he fuses the Weapons into a Mega Weapon.

After settling for a smaller apartment, the ninja go to "Grand Sensei Dareth's Mojo Dojo", and ask Dareth to let them use it to train Lloyd. Lord Garmadon discovers Captain Soto's journal in the Bounty's cabin and accidentally resurrects the ship's original pirate crew, realizing that the Mega Weapon only has the power to create. The pirates lock up Garmadon and the Serpentine and attack Ninjago City. Dareth, dressed as the Brown Ninja, jumps on board and is captured. The Ninja go to rescue him, and Lloyd does Spinjitzu for the first time. The pirates are arrested, but Lord Garmadon takes back the Bounty.

The Ninja receive an invitation for an awarding ceremony from Lloyd's old school, Darkley Boarding School, but it turns out to be a trap: the students lock them up along with the teachers and take Lloyd. Evil replicas of the ninjas, created by Lord Garmadon's Mega Weapon, learn of the Ninjas' location from Nya and go after them. At the school, the Ninjas escape only to come face to face with the Evil Ninjas. Lloyd persuades his former classmates to admit to their inner goodness, and together, they discover a way for the Ninjas to defeat their evil counterparts.

Dareth has fallen behind on his payments and a company named Darnagom (an anagram of Garmadon) intends to buy the land the Dojo is built on. The Ninjas enter the Ninjaball Run, the most dangerous race in Ninjago, hoping to cover Dareth's debts with the prize money. Garmadon also enters the race with the Bounty to prevent them from winning, but the Ninja manage to cross the finish line first in a close race. Lloyd takes the Bounty back from Garmadon.

Lord Garmadon breaks into the museum to revive the extinct Grundle using the Mega Weapon. The Ninjas interrupt him but are also affected. Reverted to children, the Ninjas are powerless against the resurrected Grundle. Just as the Ninjas are about to be eaten, Master Wu and Nya arrive with some Tomorrow's Tea, that could age them back. Lloyd uses the tea to defeat the Grundle and return the Ninja team to normal, but is aged up in the process.

Lord Garmadon uses his Mega Weapon to create a time portal, hoping to prevent the formation of the Ninja team. The Ninja follow him as he goes back in time to the day Kai met Sensei Wu. After failing to alter the timeline by stopping Nya's kidnapping, Garmadon teams up with his past self and ambushes the past Kai in the Fire Temple. The present Ninja arrive and fight back, and destroy the Mega Weapon using the past Golden Weapons. The destruction of the Mega Weapon restores the timeline.

The Ninja meet Misako, Lloyd's long lost mother, who tells them of the Overlord and his indestructible Stone Army. The venom of the Great Devourer seeps through the ground and brings a huge Stone Warrior to life, but the Ninja trick him into toppling down a bottomless pit. Meanwhile, a now powerless Garmadon returns to the City of Ouroboros to plan his next move, but the Serpentine betray him, and toss him into the sea. He washes up on the shores of the Dark Island, where he meets the Overlord, and the two join forces.

Having been crowned the new King of the Serpentine, Skales plans to undermine the foundations of Ninjago City, bringing it down into chaos. Underneath the city, the Serpentine uncovers an ancient vault, where the Stone Army rests. The Great Devourer's venom melts through the ceiling, animating the statues, who defeat the Serpentine and trap them inside. On the Dark Island, Garmadon is guided by the Overlord to the Celestial Clock, where he dons the Helmet of Shadows, starting the clock's countdown to the Final Battle.

On the Dark Island, the Overlord and his Stone Army begin the construction of a Super-Weapon, that would harness the island's, Dark Matter. The Ninja set sail for the Dark Island on the Bounty, in a quest to find the Temple of Light, where they can obtain the power to defeat the Stone Army. The ship is caught in a storm and eventually runs aground on an uncharted island with a lighthouse. In the Lighthouse, they discover Zane's father, Dr. Julien who was brought back to life by Samukai, and forced to build war machines for the Skulkin. He repairs the Bounty, allowing them to continue their journey to the Dark Island.

The Ninja arrive on the Dark Island and begin their search for the Temple of Light, while Dr. Julien and Nya build them new vehicles. They eventually locate the Temple, harness their elemental powers, bestow Golden Power on Lloyd, and are given new Elemental Swords.

Misako speculates that returning the Helmet of Shadows to its pedestal could stop the countdown and prevent the final battle. Dressed as Stone Warriors, the Ninjas escort her to Garmadon's camp, where she manages to steal the helmet. Garmadon chases after them with a giant robot. The Ninja reach the Celestial Clock but are too late to stop the countdown. The Celestial Clock powers up the Overlord's completed Super-Weapon, the Garmatron - a weapon used to shoot Dark Matter to corrupt people in Ninjago, and Nya is captured by the Stone Army.

On the coast of the Dark Island, the Stone Army deploys the Garmatron to corrupt Ninjago's inhabitants with Dark Matter, upsetting the balance between good and evil. Nya, also corrupted, attempts to stop the Ninja from following, but is subdued. The Overlord betrays Garmadon, possessing him and attacking Lloyd, who tries and fails to bring his father to his senses. The Overlord defeats Lloyd, breaking his leg and wrecking the Bounty, before opening a portal to Ninjago City and leading the Stone Army through it. The Ninja are left stranded on the Dark Island.

The Ninja return to the Temple of Light, where they find the First Spinjitzu Master's battle mech. With the help of the mech and the Ultra-Dragon, the group flies back to Ninjago City. The Overlord now morphed into a dragon, has conquered the city completely. The Ninja are outnumbered by the Stone Army, but Dareth saves them by recovering the discarded Helmet of Shadows and forcing the Stone Warriors to stand down. The Ninja climb the Overlord's tower, with only Lloyd reaching the top. Lloyd summons the Golden Dragon and defeats the Overlord, freeing the city from his control, and purging his father of the corruption.