It’s been a week since the newly-styled Emperor Garmadon seized control of Ninjago City. Amidst the chaotic, tyrannical regime, an underground resistance begins to form, led by Nya and Lloyd. Meanwhile, in the First Realm, the other ninjas with a Kid Wu find themselves shipwrecked. Attempting to ensure their survival, they soon discover that they are not alone, in the realm...

The mysterious tribe which captured Kai, Jay, and Zane, named the Dragon Hunters, take them to their leader, the Iron Baron, who seems convinced that the Ninja are Oni and killed the Ultra Dragon. They are escorted to a perilous arena and made to battle a dragon. In a bid to help their friends, Cole and Wu go undercover as Dragon Hunters. In Ninjago.

Mistaké challenges Lloyd to find his voice, convincing him to broadcast a message to inspire the people. In the First Realm, Kai, Jay, and Zane have been captured and imprisoned in the Dieselnaut and are to be used as bait for that night’s dragon hunt. Cole and Wu, still disguised, join the hunt and learn about the Firstbourne Dragon, the leader mother and queen of all dragons.

The Ninja are taken to the Dragon Hunter’s village. Planning to escape, they resolve to build a simulated Firstbourne with Cole and Wu. The resistance, led by a newly motivated Lloyd devise tactics for overthrowing Garmadon. Dareth, feeling excluded due to his lack of elemental power, convinces Mistaké to help him help obtain ‘brown power’.

Harumi leads an attack on the secret headquarters of the resistance. Now sundered, and living in the slums, those remaining discover a secret about Mistaké. The Ninja, now free from the hunters, wake to find a now teenager Wu remembering more about his past. Finding an unlikely ally in Heavy Metal, the Iron Baron's second-in-command, who reveals himself to be a woman named Faith.

Mistaké reveals her true origins to the Resistance and teaches Lloyd that he must transform one final time into the great leader he is destined to become. Meanwhile, Emperor Garmadon embraces Harumi as his daughter of darkness and sends her to capture Lloyd, but she ends up being captured herself. Continuing on their journey with Faith through the desert, the team venture into Oni territory.

Faith teaches the Ninja to use vengestone harpoons and Wu to ride a dragon, but when they are found by the Dragon Hunters who capture Faith, Wu and the Ninja are forced to continue their journey alone. Meanwhile, in Ninjago, the Resistance keeps Harumi hostage at their hideout and come up with a plan to have Mystaké disguised as her and Skylor as a prisoner goes to Garmadon's base.

After trying to rescue Faith, the Ninja and Wu get captured. Faith reveals the Iron Baron's lies to the other Dragon Hunters, while Wu ages up to a young adult and regains all his memories. He makes a deal with Iron Baron who, in exchange for the Dragon Armor, promises to send the Ninja back home. In Ninjago, after being discovered, Mistaké reveals her true Oni nature to Garmadon and confronts him.

After Harumi's death, Garmadon angrily begins destroying the entire Ninjago City with Colossus, while Lloyd and the others head to a more remote side of the city, waiting for Wu and the other Ninja to return. They run into Ultra Violet, whom Nya has a fight with and gets injured, but they manage to defeat her and continue their path. In the Realm of Oni and Dragons, the Dragon Hunters release the Ninja and Faith after realising that Iron Baron showed his true colors and cares only about himself.

Wu and the four Ninja are finally back home and reunite with their friends. Nya and Dareth takes Skylor to safety, while Kai, Jay, Zane, and Cole rescue the civilians and fight Colossus, and Lloyd and Wu confront Garmadon. The Elemental Masters and the Ninja's other allies escape from Kryptarium prison and help the Ninja defeat Colossus, while Garmadon defeats Wu and the Firstbourne Dragon, leaving only Lloyd to fight him.