Lloyd visits Garmadon at Kryptarium prison, who tells him that "The Darkness", which is to destroy all the realms, is soon going to arrive in Ninjago soon. Meanwhile, Cole, Zane and P.I.X.A.L go to the Ninjago harbour to receive an award, which they are surprised to discover is a rebuilt "Destiny's Bounty". Faith, who has been severely injured, arrives at the monastery to warn Wu and the ninja that the darkness has consumed the Realm of Oni and Dragons and is heading for Ninjago next. After Ninjago City is covered in a cloud of darkness, Lloyd reluctantly decides to free Garmadon from Kryptarium Prison so that he may help the ninja combat this new threat. 

Having freed Garmadon from prison, the ninja are beset by doubts, particularly Lloyd. After a provoked battle results in the return of Garmadon's powers, Lloyd and Garmadon enter the cloud of darkness in an effort to stop the Oni invasion. After encountering a pair of Oni, the two reach the Realm Crystal, but are too late, as the Oni's leader, Omega, is released upon Ninjago. 

While Lloyd and Garmadon try to escape the Oni, P.I.X.A.L. prepares to enter the darkness to save them. Meanwhile, the Ninja tend to a distress call, but Cole ends up falling into the darkness. Garmadon and Lloyd obtain the Armour of the Golden Master, and Nya tells Kai he must melt the armor back into the Golden Weapons. 

The Ninja return to the Monastery of Spinjitzu, in the last stand between them and the Oni. Kai recreates the Golden Weapons to help the team fight the Oni. In the midst of the battle, Cole, who has survived the darkness, returns to the monastery as well. The Ninja, Wu and Garmadon eventually use the Tornado of Creation to defeat the Oni, but this causes Lloyd to pass out. He sees his grandfather, the First Spinjitzu Master, in a vision before waking up, while Garmadon departs in silence. The Ninja and their allies celebrate their victory by putting their hand together on the Monastery’s wall.