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Holding Arin and Sora at gunpoint and in restraints, Dr. LaRow laments Sora's defection from Imperium. Arin is confused by LaRow's addressing Sora as "Ana", until his friend explains that it was her birth name. After accusing Sora of using dragons for power just like her, though Sora argues that Riyu voluntarily provides her with power, LaRow brings up surveillance video of the battle outside to make the two captives watch as their friends are defeated. However, they then watch the Imperium Monastery rise up from beneath the city and open to admit Kai, Nya, and Zane.
Taking advantage of this distraction, Arin and Sora confront their captors, while outside Lloyd reunites with his friends and gives them the essentials of their situation. Though Kai is baffled by Wyldfyre's apparent power over fire, the Ninja quickly join in the battle on the side of the dragons. Dr. LaRow is quickly overcome by Sora and Arin, but Jordana proves a more aggressive opponent. When Sora is baffled by her hostility, she reveals that she was a classmate of Sora's-then Ana's-who always felt overshadowed by her. Much to her annoyance, she continues to be rated behind Sora, who also still has no memory of Jordana.
Unable to overcome the Photacs, the Ninja and Wyldfyre decide to retreat inside the Imperium Monastery with the dragons, hoping to give Arin and Sora the time they need to rescue Riyu and enact Sora's plan to stop the Photacs. Rapton tries to prevent this escape but fails, and Dr. LaRow then comes running to alert Ras to Arin and Sora's resistance. The two Ninja trainees overcome Jordana, but Ras arrives before they can free Riyu from his cell. Infuriated, Empress Beatrix orders Rapton to use the Photacs to break down the doors of the Imperium Monastery, which the Ninja determine they must use to get the dragons to safety.
Zane analyzes the gate leading to the Monastery of Spinjitzu and determines that it lacks the power to transport all the dragons. However, he then detects a massive power source beneath the Imperium Monastery, which Lloyd finds a passage to. Rather than surrender to Ras, Arin and Sora engage the tiger-like warrior while Lloyd and Zane make their way to the power source. Inside a subterranean chamber, they find a massive forcefield.
Despite some early success, Arin and Sora struggle against Ras' might, while Lloyd and Zane discover that the forcefield contains a massive-and massively powerful-dragon. However, as they are attempting to release it, the dragon-who reveals himself as one of the Source Dragons-forbids them from doing so. As he explains, his capture has stabilized the Merged realms, and his release has the potential to destroy them. Knowing of their plight, he offers to imbue Lloyd with some of his vast power, which will be enough to accomplish what they seek.
Lloyd accepts, and is then shown a strange vision in which he sees large glowing symbols, what appears to be a Ninja graveyard, and finally a massive dragon. Ras, meanwhile, finds that he has unwittingly helped Sora free Riyu, who charges up her powers and enables her to defeat and confine the villain. The pair and Arin then run out, while Lloyd arrives back in the Imperium Monastery suffused with power from the Source Dragon. He then powers up the gate to the Monastery of Spinjitzu, enabling the dragons to escape through it.
The Imperium forces break through just after the dragons can escape, but before they can attack the Ninja Sora arrives and uses her powers to disable the Photacs. The Ninja and Wyldfyre then make their own way through the gate to the Monastery of Spinjitzu, leaving behind a humiliated Rapton and a furious Beatrix. Sometime later, Lloyd awakens back in his room at the Monastery of Spinjitzu, somewhat woozy after his ordeal. Walking outside, he finds Sora training and now determined to harness her Tech powers, regardless of whether they are hers of Riyu's. She then brings him up to speed on what's happened in the days he's been asleep, including the fact that Wyldfyre and several of the dragons are now living the strange new chambers beneath the monastery.
After a happy reunion with the other veteran Ninja, Lloyd goes to speak to a downcast Arin. The youngster explains that he feels that Lloyd no longer needs him with his friends back, something that Lloyd is quick to refute. Arin also notes that since losing his hisparents, he's been looking for a new family-which Lloyd assures him he has found. Back in Imperium, Beatrix rejects Ras' suggestion that they hunt down more dragons, wishing instead to find and punish the Ninja for daring to defy her. She orders an aghast Ras imprisoned, and then reveals a mech with which she intends to become personally involved in the coming battles.
