This article needs to be built up. This article lacks substantial content. You can help Brickipedia by "adding on some bricks." In other words, it needs to be expanded. After you expand the article, please remove the "Expand" template. Further information might be found on the talk page.
Following the evacuation of Ninjago City, Wu and Zane discover that the Dark Island has appeared on the horizon. With the Stone Army having disappeared, Zane decides to send his Falcon to investigate the island to see if Garmadon might be responsible for the recent incidents. Meanwhile, the rest of the Ninja work on the Destiny's Bounty, which was badly damaged in their escape, while Lloyd laments his inability to stop the stone warriors.
Misako then introduces the group to some of her research, which indicates that the Ninja may be able to regain their Elemental Powers and unlock Lloyd's true potential by traveling to the Dark Island and finding the Temple of Light. The Bounty, though unable to fly, is readied for a sea voyage, and the Ninja part ways with Ed and Edna Walker, the Royal Blacksmiths, Dareth, and the Ultra Dragon. Zane is somewhat saddened, as he has no one to bid farewell to, but cheered when several fans-including Rufus McCallister-appear to see him off. The Bounty is soon underway, and the Ninja begin to question what might be waiting for them on the island.
Zane then receives a transmission from his Falcon, showing footage of the Dark Island, but the robotic bird is shot down by a Stone Swordsman. The crew of the Bounty runs into a storm, while on the Dark Island Garmadon and the Overlord oversee the mining of the island's dark matter. As the Overlord explains, the substance has the ability to corrupt any being who is exposed to it, and will enable them to build a might superweapon. As the Ninja desperately try to make it safely through the storm, they are attacked by Starteeth, and the creatures begin to consume the ship.
The Ninja make their way through the storm but end up with a badly damaged, rudderless ship, which drifts onto a small island with a lighthouse-like structure atop it. As the crew investigates, they are stunned when the door to the structure is opened by none other than Dr. Julien, Zane's supposedly deceased creator. Their meeting is disrupted by an ominous roar from the nearby ocean, and Julien ushers them inside quickly. After checking the nearby sea with a security camera, he leads the group to the top of the lighthouse, where he has established a neat living space with his small robot assistant, Tai-D.
Zane questions how his father can still be alive, as his last memory of Dr. Julien is of him perishing of old age. Julien reveals that, after he turned off Zane's memory switch, he was revived by Samukai and taken captive by the Skulkin leader. Julien was brought to the lighthouse prison and blackmailed into designing weapons for the undead warriors. As Julien then explains, Samukai also chained a Leviathan in the nearby sea in order to insure that Julien couldn't escape. The creature checks in on Julien, and after narrowly managing to fool it, he cooperates with the Ninja to get the Bounty airworthy again.
That night, Zane asks if Dr. Julien can remove his memory switch, as he doesn't wish to forget his father ever again, and Julien assures him that neither of them will. As the Leviathan rises, the crew of the Bounty make a desperate bid to escape, but the creature is too powerful for them to fight off. Zane realizes that the Leviathan will continue to stop them so long as it remains chained, and dives into the sea to rectify the situation. Making use of the Starteeth infesting the nearby waters, he managed to break the Leviathan's chain just as it's about to drag the Bounty underwater. Zane returns to the ship, and he and his friends watch as the Leviathan, like Julien, departs its prison.
Cole whistles the along with the soundtrack at one point.