On the Dark Island, the Stone Army is preparing for their war on Ninjago, mining a mysterious powder that the Overlord says is concentrated Evil. He tells Garmadon that they need a Super-Weapon unlike anything ever seen.
Whenever the Overlord and leave for a bit he's training his precious little daughter, so she doesn't accidentally destroy anything because of her new powers that she can't control. Ever since his wife died he was so angry and kinda sad. Until he learned his daughter was still alive and only 5.
He had found a way to communicate with his daughter while she was in Ninjago. His daughter was the most important thing to him right now. He won't loose her, so it is important that his daughter is by his side when he takes over.
She is having a hard time controlling her powers but it's ok, he'll just have the stone army protect her. Everything will be fine. He hears she had a bad reputation back in Ninjago. Quite the little trouble maker she was.
Back in Ninjago, Zane sends his falcon to investigate the island. while the other Ninja and Nya try to repair the Bounty. It is hopeless, and the Ninja despair of defeating the Stone Army. It is then that Misako tells them of the Temple of Light, where the Golden Weapons were imbued with their powers. There, the Ninja can unlock their True Potential on their own and supercharge Lloyd, enabling him to defeat the Stone Army.
They set sail for the Dark Island on the Bounty, leaving Dareth to guard the escapees from Ninjago. During the voyage, the falcon reaches the Dark Island and all are witness to it being attacked and seemingly destroyed. The Bounty is then struck by a storm and attacked by starteeth, vicious ship-eating creatures that leave the Bounty without any steering, a damaged mast and a hole in their side.
They eventually run aground on an uncharted island with a lighthouse. There, they find Zane's father, the Tinkerer. While he entertains them, the Tinkerer explains that after he flicked Zane's memory switch and died, Samukai arrived and brought him back to life, forcing him to construct their advanced war machines. To make sure he did not escape from the island, the Skeletons chained a Leviathan to keep guard.
Though Zane is glad to see his father again, the Tinkerer was always afraid that Zane might be ashamed of him for creating the weapons for the Skeleton Army, but Zane soon dispels his fears. Zane's father agrees to repair the Bounty, but just as they are setting off, the Leviathan attacks. Zane dives overboard and cuts the chain holding the creature in place.
In return for this, the Leviathan releases the Bounty. When asked by Sensei Wu how he knew the beast would do that, Zane explains that nothing deserves to be held captive, even a monster. With the creature freed and the Tinkerer on board and the Bounty once again airborne, continues its journey to the Dark Island.