The ninja return to the Destiny's Bounty to decide what to do after failing to stop the final battle. The ninja decide to take on the stone warriors face to face to allow Lloyd to fight Lord Garmadon. They arrive at the stone warriors' camp to find it deserted, and discover a trail of large of vehicle treads heading for the coast. Due to its size, they figure it to be Garmadon's Super Weapon, the Garmatron. Zane's father decides to stay back at the Bounty, stating that he is an inventor, not a fighter. He wishes them good luck, and tells Zane that he hopes he will come back in one piece.
As the ninja run towards the coast, they share memories about all the things they've done, worrying that this could be their last mission. Suddenly, Nya jumps in front of them, revealing herself to have been turned evil after Garmadon tested The Dark Matter on her. Cole, Kai, Jay, and Zane stay behind to fight Nya, while Sensei Wu, Misako, and Lloyd continue to the coast. Lloyd attempts to stop Garmadon, whose master plan is to launch Dark Matter at Ninjago, so that the balance will shift and the Overlord can cross between the islands. Lloyd fails to stop this, and Garmadon manages to fire on Jamajakai village and Kai's village. Garmadon states that he can finally turn Ninjago into his own image, but the Overlord claims that Ninjago was always his, and then takes over Garmadon's body, just as the rest of the ninja arrive.The final battle begins and Lloyd battles the Overlord. During the battle, Lloyd tells Garmadon to fight the Overlord back. Garmadon attempts to take control of his body, but fails, telling his son to stay strong. The Overlord blasts Lloyd back using dark energy and knocks him out in the process.
Just before the Overlord can fire at Lloyd with the Garmatron, Zane's father flies the bounty in front of the missile and jumps off the bounty as it crash lands, stating "That went well." The Overlord decides not to bother with the ninja, and he, the stone army, and Nya cross through a vortex to Ninjago City before the ninja can follow. Lloyd wakes up and discovers that he has a broken leg. He finds a piece of wood with the symbol for destiny and concludes that destiny must want them to fight another day.
1. Farewell the Sea · 2. The Call of Home · 3. The Shape of Nya · 4. A Mayor Problem · 5. Public Enemies 1, 2, 3, 4, and 5! · 6. A Painful Promise · 7. Ninjago City vs. Ninja 8. Kryptarium Prison Blues · 9. Hounddog McBrag · 10. The Benefit of Grief · 11. The Fifth Villain · 12. The Council of the Crystal King