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A group of four friends is driving home from dinner at Grab-Barg's restaurant and discussing the changes in the world since the Merge and the disappearance of the Ninja when a Merge quake occurs. The group's car goes off the edge of the bridge, but they are saved from harm by the arrival of the Ninja on their newly acquired dragon mounts. Returning to the Monastery of Spinjitzu, they settle their mounts into the new dragons stables beneath the monastery. Arin comments on the appearance of the structures, wondering if it is some kind of fate, a notion that Sora discounts.
Despite many offers for her to do so, Wyldfyre refuses to join her new friends in the monastery, preferring to live in the stables with Heatwave. Lloyd, meanwhile becomes occupied with keeping the monastery in order, feeling it his duty to handle the task single-handedly as he evidently feels Master Wu always did. However, his efforts are disrupted and hampered by Sora practicing with her mech and Wyldfyre's temperamental reaction to Kai attempting to train her. All of this is interrupted when Zane, after multiple attempts, finally makes it clear that the increasingly frequent Merge quakes have the potential to destroy the new merged realm.
After Zane notes that he sees no way of preventing this from occurring, Nya sees something familiar on the map of the merged realm. It proves to be something she uncovered during her research in the Cloud Kingdom: a location that may hold the key to stopping the Merge quakes. The Ninja quickly set out on their dragons to investigate, unaware that Rapton is spying upon them. Meanwhile, back in Imperium, Empress Beatrix makes an announcement to her citizens-including Sora'sparents, a captive Lord Ras, and the Imperium Teen Protection Force-claiming that no dragons have escaped.
Percival and his friends question this announcement, having observed the dragons getting into the Imperium Monastery. Behind the scenes, Dr. LaRow informs Beatrix that their power is depleted without the captive dragons, due to their inability to drain power from the Source Dragon they have captive. She attempts to convince Beatrix to lower power usage, but Beatrix refuses, believing that her citizens must be kept content to insure their compliance with her rule. The Ninja, after making their way through the giant World Trees, arrive at a mysterious temple with a locked door.
After Zane analyzes the combination lock and is unable to determine the solution, the Ninja in training stumble upon the idea of three people operating each of the three levers. This gets them inside, but Wyldfyre's proposal that she and Kai blast open a couple of doors results in a pair of ghostly beings starting to attack them. As Rapton sneaks into the temple past the dozing dragons, the Ninja find that they can do no harm to their attackers. However, Lloyd spots a fallen altar and sets it to rights with his friends' help.
Lloyd's instincts prove correct, and the ghosts unite into the Spirit of the Temple, who thanks the Ninja for repairing the damage done by a Merge quake. He explains that he and the temple were created by the First Spinjitzu Master, who he reveals also created a number of realms besides Ninjago. The First Spinjitzu Master long ago learned of the coming Coalescence-aka the Merge-and approached the Source Dragons for help in stopping it. Together they created the Dragon Cores, which were used to stop the first Coalescence before being hidden away to keep them out of evil hands.
Realizing that the cores may have the ability to stop the Merge quakes, even if it's too late to prevent the realms from merging, Lloyd fulfills the spirit's requirement that a descendant of the First Spinjitzu Master ask for knowledge of the cores' locations. These prove to be the Mother Garden, the Pinnacle of Crystals, and the Wyldness. Unfortunately, after the Ninja make their way out of the temple, Rapton is able to discover this information as well. Back at the monastery, Lloyd attempts to plan out the mission to retrieve the cores, but continues to try and take on too many tasks by himself.
Arin and Sora, having become concerned about Lloyd, introduce him to Mr. Frohicky, whom they have asked to put his organizational skills to use helping take care of the monastery. After his latest solo chore attempt fails miserably, Lloyd takes the hint and agrees to appoint Mr. Frohicky as Assistant Keeper of the Monastery. Rapton reports on his findings to the Empress, and she decides to go after the Dragon Cores herself. However, her intention is not to prevent the Merge quakes, but to use them as a weapon in her bid to eliminate the Ninja.
