The ninja help repair Ninjago City although they have lost their elemental powers. Nya informs them that she has found a real-estate agent who will help them find a place to live. Lord Garmadon persuades the Serpentine to follow him, and recreates the Bounty from its remains. The ninja find a luxurious apartment with a training-room and although it is expensive, they decide to get jobs to pay for the rent. 

The ninja find "Grand Sensei Dareth's Mojo Dojo", where Dareth agrees to let them use it to train Lloyd. Lord Garmadon discovers Captain Soto's journal in the Bounty's cabin and accidentally resurrects the original pirate-crew of the Bounty using the Mega Weapon. Lord Garmadon realizes that the weapon only has the power to create, while the pirates lock him up with the Serpentine. 

The Ninja receive a message from Lloyd's old school, Darkley Boarding School, inviting him to receive an award. Meanwhile, Lord Garmadon creates evil impersonations of the Ninja to deal with them. The Ninja arrive at the school and are surprised to see none of the students or teachers. Indeed, the whole award is revealed to be a trap and the Ninja are locked in a room with all the teachers, and Lloyd is tied up. 

Lloyd is training in Dareth's dojo when a wrecking ball crashes through the wall. It is revealed that Dareth has fallen behind on his payments and a company named Darnagom will buy the dojo, but Zane discovers Garmadon's part behind this being that Darnagom is Garmadon arranged. The Ninja learn of the grand prize of the Ninjaball Run, the most dangerous race in Ninjago, and decide to enter the race. The next day, the race starts promising indeed.

Lord Garmadon arrives at the museum planning to revive the extinct Grundle to hunt the Ninja. The Ninja interrupt his plan, but are affected by the power of the Mega Weapon and turned into kids. Moreover, the Ninja realize the Grundle must have been revived after all and escape the museum. The Ninja call Lloyd to meet them and inform him of the situation. Lloyd calls Master Wu and Nya back at the Destiny's Bounty, telling them what happened. 

After the Ninja foil his latest plan, Lord Garmadon uses his Mega Weapon to go back in time and prevent the formation of their team. Unknown to him, the Ninja have come with him back 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 amboushes the past Kai in the Fire Temple. The present Ninja arrive and fight back.

Garmadon, now powerless, returns to the City of Ouroboros to plan his search for the legendary Dark Island, but the Serpentine soon betray him, pushing him into the sea by a helicopter while Skales is declared their leader. Meanwhile, the Ninja meet Misako, Lloyd's long lost mother, who tells of the existence of the Overlord and his indestructible Stone Army. 

Skales is crowned the new Snake King and plans to dig the foundations of Ninjago City, bringing it down into chaos. However, the Serpentine discover a secret vault where the Stone Army rests, before the Great Devourer's venom melts through the roof and brings the statues to life. They defeat the Serpentine and trap them inside. Then, they rise up to the city which begins to evacuate.

On the Dark Island, the Overlord tells Garmadon that they need a Super-Weapon unlike anything ever seen. Back in Ninjago, Zane sends his falcon to investigate the island. Misako tells the Ninja of the Temple of Light, where they can obtain powers to defeat the Stone Army. They set sail for the Dark Island on the Bounty, but the ship is then struck by a storm.

The Ninja arrive on the Dark Island and search for the Temple of Light, while Dr. Julien and Nya build new vehicles for them. Then, the Ninja infiltrate Garmadon's camp and Jay locates the temple. After escaping, the Ninja head for the temple, where they are gifted with Elemental swords and kimono, and with their new powers, the Stone Army is defeated.

Misako reveals that there might be a way of avoiding the Final Battle: returning the Helmet of Shadows to its pedestal. The Ninja escort Misako into Garmadon's camp impersonating Stone Warriors, where she manages to steal the helmet, but they are spotted and Garmadon, enraged, uses a giant robot to chase after them. The Ninja get to the Celestial Clock and try to find the Helmet's pedestal, but are too late.

The Ninja return to Garmadon's base but find it deserted, as everyone has left for the coast to use Garmatron to upset the balance between good and evil. The Ninja follow, but are stopped by Nya, polluted with Dark Matter. They eventually overcome her and reach the coast, but Garmadon uses Garmatron, infecting the balance. The Overlord then betrays Garmadon, possessing him and attacking Lloyd. Lloyd tries to bring back his father. 

As the Overlord conquers Ninjago, the Ninja return to the Temple of Light, where they find the First Spinjitzu Master's battle mech. With the arrival of the Ultra-Dragon, the group flies back to Ninjago City, which is now possessed by Overlord, who has morphed into a dragon. The Ninja fight the Stone Army, but in the end, they are saved by Dareth, who uses the Helmet of Shadows to control the army. The Ninja climb the tower where the Overlord is.