The four ninjas learn that evil forces have begun to reappear when Lord Garmadon forges their lost Golden Weapons into a Mega-Weapon with unimaginable powers just as Ninjago's reconstruction work gets underway.
The ninjas must prevent the vicious Black Bounty's original owners, Captain Soto and his pirates, from plundering Ninjago City when Garmadon accidentally revives them after they were once thought to be dead.
The ninjas find out that the invitation to return to Darkly's Boarding School is a trap set by Lord Garmadon and his sinister duplicate ninjas, which Garmadon's new Mega-Weapon has produced.
A company called Darnagom plans to purchase the land on which the Dojo is constructed after debts have accumulated on Dareth, so the Ninjas compete in Ninjago's race, the Ninjaball Run, to pay off Dareth's debts with the winnings.
To use the Mega Weapon to bring back the extinct Grundle, Lord Garmadon infiltrates the museum but gets interrupted by the ninjas, who are also impacted. The ninjas, now transformed into kids, are helpless against the living Grundle, so Master Wu and Nya show up to help them.
The ninjas pursue Garmadon and attempt to stop him with the Golden Weapons from the past to combat Garmadon's Mega-Weapon as he travels back in time to undo the past and remove the ninjas from the future.
Garmadon manages to locate an evil Island that is claimed to contain evil abilities while the ninjas square off against an exhibit of a Stone Samurai Warrior that has been brought to life by the toxic venom from the Great Devourer.
The rest of the Stone Army, which the Devourer's deadly venom has brought to life, pursues the ninjas as they attempt to escape. However, things quickly spiral out of hand when Garmadon appears with a "Helmet of Darkness" and takes over command of the Stone Army.
The Starteeth, or barnacle-shaped starfish, assault the Ninjas, Lloyd, Sensei Wu, and Misako as they go to the Dark Island in search of a "Temple of Light" that can restore the Ninjas' powers, and the starfish begin devouring their ship.
The ninjas finally make it to the Temple of Light, where they concentrate their powers and focus them on Lloyd, making him stronger than he could have ever dreamed, after fending off Garmadon's Stone Army.
A Super Weapon capable of destroying all of Ninjago is produced after the ninjas' failed attempt to bring Garmadon's "Helmet of Darkness" back to its perch above the Celestial Clock to stop the start of the last fight between Lloyd and his father.
The balance gets unintentionally upset when Garmadon uses his new Super-Weapon to make Jamakai Village evil, allowing the Overlord's spirit to cross over and take control of his body.
The terrible Garmadon Super-Weapon has cast complete darkness over Ninjago, but Lloyd and the ninjas manage to prove that light is stronger than darkness, and the final and decisive battle has begun.