Since Lord Garmadon's defeat, Ninjago City has been rebuilt. However, when Lloyd visits his father in Kryptarium Prison, Garmadon warns him that the "Bringers of Doom" are coming, but Lloyd refuses to listen. Meanwhile, the ninjas are presented with a newly rebuilt Destiny's Bounty. Garmadon's warnings soon prove to be justified when the Oni demons invade Ninjago by entering through the Realm Crystal. Darkness spreads across Ninjago City and petrifies anyone who touches it. On board Destiny's Bounty, the ninja race to Ninjago City to rescue the citizens from the darkness. However, when the ninjas use their elemental powers against the dark cloud, they discover that they have no impact. Lloyd visits his father in Kryptarium Prison for advice. With no other choice, the ninjas release Garmadon from prison and form an uneasy alliance with him in an attempt to defeat the Oni and save Ninjago from the darkness.
Back on the Bounty, Garmadon tells the ninja that the only way to save Ninjago is to destroy the Realm Crystal, which is located at Borg Tower. Lloyd and Garmadon agree that they alone can safely venture into the darkness and not be petrified because of their Oni blood. While Lloyd and Garmadon enter the darkness, the ninjas receive a distress signal from the NGTV building. They decide to go and help the people trapped there, while Pixal stays behind to help Lloyd and Garmadon. When Lloyd and Garmadon reach the Realm Crystal, Garmadon tries to destroy it, but the Omega, the Oni leader, confronts them.
While fighting the Omega and the Oni, Lloyd destroys the Realm Crystal with the Sword of Sanctuary, but it fails to stop them. Lloyd and Garmadon then find the Armour of the Golden Master and realize that it causes the Oni to recoil. They escape from Borg Tower, taking the armor with them, and are picked up by Pixal As the ninja are helping people escape at the NGTV building, Nya accidentally pushes the thrust lever the wrong way and Cole, who is hanging from a ladder, falls from the Destiny's Bounty into the darkness, seemingly killing him.
After Lloyd and Garmadon return, the ninjas fly to the Monastery of Spinjitzu onboard Destiny's Bounty so that Kai can reforge the Golden Weapons, believing that this can stop the Oni. When the Oni attack the monastery, a battle takes place outside the walls. During the battle, the ninjas are slowly overwhelmed by the growing Oni horde, but Cole arrives in the Earth Driller and the ninjas realize that he has survived. Jay then asks Nya to be his "Yang," and Nya happily accepts, without hesitation. When all hope seems lost, the ninjas, Wu, and Garmadon join forces and use Spinjitzu to make the Tornado of Creation, which results in the Oni's destruction. After the battle, Lloyd experiences a vision where he meets the First Spinjitzu Master, who thanks him for saving Ninjago. Garmadon leaves to start his own comic book series named: Garmadon, as the ninja celebrate their victory and share history by placing their handprints on the wall mural of the Monastery of Spinjitzu.