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Looking down on Arin and Sora, Lloyd questions the whereabouts of the "Ninja" he saw doing Spinjitzu earlier, only to learn that it was Arin. As the three of them engage Rapton and the Imperium Claw Hunters, Lloyd is astonished by Arin's untrained Spinjitzu, while Sora discovers that the powers she used previously have apparently vanished. Arin then frees the dragon he and Sora met previously, and the creature quickly gives Sora a boost, allowing her to once again use her new abilities. However, her inexperience causes her to turn the Imperium weapons into bombs, and the freed captives and their rescuer quickly jump off the train.
Lloyd struggles to process all these developments, while the dragon uses some rubble to make a sculpture of his home. Lloyd takes his new friends to the Monastery of Spinjitzu, which has some bizarre new features following the Merge. Searching through a number of messages from Kai, who has been exploring their newly expanded world, they find the location the dragon was trying to lead them to: the Land of Three Mountains. In order to reach it, Lloyd decides that they'll take the new Destiny's Bounty, which is yet to be finished.
Sora briefly attempts to use her new powers to finish the task, but when this proves unsuccessful she returns to her old methods. As she works, Arin explains how they came together to Lloyd, who returns the favor by explaining what happened to him before and after the Merge. Master Wu, as he explains, was apparently aware of the event ahead of time, but it caught him and the Ninja by surprise. After their short-lived efforts to rescue civilians, they were caught up in the Merge, and Lloyd found himself alone back at the monastery. Unfortunately, Lloyd was unable to piece together anything from Wu's destroyed notes except a mysterious reference to Source Dragons.
Some weeks afterwards, the old Destiny's Bounty returned carrying Kai, who had been transported to a newly created island. The two Ninja soon discovered that the merged realms were afflicted by "Merge quakes", aftereffects of the original event that can only be countered by Elemental Power. Kai decided to search the expanded world for answers in the old Bounty, while Lloyd remained at the monastery to oversee things. During his patrols, he spotted Arin doing Spinjitzu.
Arin, excited, believes that they were meant to meet and that Lloyd is meant to train him and Sora as Ninja. Lloyd doubts his qualifications, but is soon distracted as Sora gets the new Bounty flight worthy. They quickly make their way to the Land of Three Mountains, only to be attacked by the Claws of Imperium who have followed them there. The Bounty is shot down, but saved from a crash by the arrival of a Dragon Matriarch that carries the ship to safety.
The dragon interrogates the humans, and from her communications they learn that their small friend is named Riyu. The matriarch, initially believing that the three are in league with the dragon hunters, decides to let them prove their good intentions by helping fight the enemy, who are attacking the other members of her herd. Unfortunately, after she saves Sora from being thrown off a cliff by Rapton, the matriarch herself is targeted. After she is subdued, Rapton reports to Lord Ras, only for Lloyd to approach and engage the Imperium soldiers.
Lloyd explains to the matriarch how Riyu has been empowering Sora, and suggests that she enhance his powers using the same method. She does so, and Lloyd's supercharged Spinjitzu proves more than a match for Rapton and his hunters. However, Ras apparently expected and even desired this outcome, and makes his way back to Imperium rather than remaining to assist Rapton. Inspired by his new friends and conversation with the matriarch, Lloyd decides to teach Arin and Sora.
The youngsters attempt to say goodbye to Riyu, but he is intent on remaining with his new friends, which the matriarch grudgingly allows. Meanwhile, Lord Ras reports to Empress Beatrix regarding Lloyd's bonding with the Dragon Matriarch, which is apparently in harmony with their plans to locate the Source Dragons. Beatrix then gloats to one of these creatures, imprisoned below Imperium, and anticipates the power that will soon be hers.
