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As a MergeQuake rift opens over Imperium, Rapton bemoans their imminent demise while Dorama rejoices until Rapton points out his own probable fate. Lloyd, Nya, and Zane attempt to reason with the deranged Empress Beatrix, but she refuses to believe their claims about what the MergeQuakes will do. Wielding the weapon with her mech, she begins opening rifts left and right, using the weapon's power on her own citizens. As a storm begins to stir around them, all of the Ninja reunite and launch into battle against the mad Empress.
Unfortunately, Wyldfyre is soon drawn into one of the rifts when Beatrix fires on her, and the Imperium Teen Resistance Force begin leading civilians to safety underground. Percival, sadly, is soon drawn into a rift as well. However, Sora hits upon the idea of using her powers to disable the weapon, and heads towards Riyu for a power boost. Unfortunately, the Empress soon sends him flying into another rift, and then targets Sora herself. Seeing this, Arin grabs a rock and empowers it with Spinjitzu to launch it at Beatrix's mech, blasting a hole through it but not disabling the machine.
A power failure in Imperium's prison allows Lord Ras to escape his cell, but Kai's attempt to avenge Wyldfyre sees him drawn into a rift as well. Rapton is also drawn through a rift as he attempts to assist Nya in attacking the Empress, but Lloyd brings the team mechs into the battle to help even the odds. As Sora runs through the chaos, herparents arrive and demand that they come with her. Sora learns that in spite of her broadcast, her parents still believe that the Empress is good, and she realizes that she's always believed she had to prove herself to them.
Lloyd and Arin's mechs are drawn through the portal, but as Beatrix prepares to subject Lloyd and Arin to the same fate, Sora chooses her new family over her old one. She thus is able to access her elemental powers on her own for the first time and rips apart the MergeQuake weapon, allowing Arin to use Spinjitzu to send Beatrix flying into one of her own rifts. Unfortunately, their victory seems hollow, as Beatrix's efforts have triggered the apocalyptic event Zane has foreseen for some time. As the Crossroads is also caught up in the chaos, the Ninja take to the skies aboard the Destiny's Bounty only for it to be damaged and start falling.
Zanth deposits Sora on the Bounty and then displays a previously unknown talent by growing to an immense size and carrying the vessel on her back. She and Jiro bring the Ninja to the Crossroads, where they immediately begin assisting citizens like Lobbo, Grab-Barg, and others. As Arin assists, a rift opens up and he briefly glimpses hisparents before it closes again. Lloyd notes that if they are to have any hope of stopping the MergeQuakes, the Spirit of the Temple said that they would need all three Dragon Energy Cores. Fortunately, Mr. Frohicky-having been contacted by Zane-arrives in Zane's car to add the one Lloyd and Arin retrieved to the two recovered from Imperium, though Zane has to assist him in stopping.
Despite having the three cores, the Ninja have no idea how to use them, until a remark of Zane's about Source Dragons inspires Sora. She reminds Lloyd that he was chosen as a conduit by the Source Dragon beneath Imperium and encourages him to try channeling the power of the Dragon Cores. In spite of the potential danger to himself, Lloyd agrees, but initially struggles due to the surrounding chaos until Arin reminds him of his teachings to them. Lloyd himself is then reminded of his own lesson from Master Wu, and is able to channel the power of the Dragon Cores to halt the MergeQuake storm.
With the rifts closed, various victims of Beatrix's actions begin safely reappearing, including Wyldfyre, Kai, Riyu, and Percival. The inhabitants of the Crossroads celebrate, both for their rescue and for the realization that the Ninja have returned. Rather than taking the Dragon Cores back to the Monastery of Spinjitzu, Lloyd once again visits the Source Dragon beneath Imperium. He offers them to the Source Dragon so that the creature can safely leave his prison and is stunned when the dragon reveals that he and his fellow Source Dragons are the source of all Elemental Power.
The Source Dragon marvels at Lloyd's willingness to give up such power for a being he barely knows, and muses that perhaps a mysterious "he" was correct in his judgement of Lloyd. He then questions the presence of Riyu, who accompanied Lloyd, and notes that the young dragon is special. Accepting Lloyd's offer, he departs, noting that he and Lloyd may meet again. Lloyd and Riyu then return to the monastery, where Heatwave, Jiro, and Zanth are celebrating as the others work at various tasks.
Seeing Sora at work on her mech, Riyu goes to her; however, having realized what was holding her back before, Sora is now determined to unlock her powers by herself. Arin, meanwhile, is continuing his attempts to master the art of imbuing objects with Spinjitzu, but continues to be frustrated. Lloyd comforts him, and encourages him to turn his worries to a purposeful use. Kai works with Wyldfyre regarding her own abilities, and then makes a curious observation that leads him to believe that her Elemental Powers, though similar to his, are indeed different.
As the older Ninja contemplate Cole's communication from Master Wu and departure, Arin breaks out a celebratory batch of pies. Unseen by the Ninja, Wu's spirits observes the group before departing. Back in Imperium, Sora's sorrowful parents observe the institution of a new system of government, while Jordana gripes over her apparent failures. However, she is then approached by Lord Ras, who praises her work with the Source Dragon and notes that his "master"-who was never Beatrix-has other plans. Jordana is then offered a place with him and his master, and reveals that she has a small quantity of the Source Dragon energy she drained in her possession that will further their plans...
