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The Imperium Teen Resistance Force lead the Ninja through the streets of Imperium, with Arin noting the strangeness of working with Percival and his friends after their previous hostility. Lloyd questions Percival about the recent explosion, which Percival notes came from the Advanced Systems Lab. Unfortunately, before they can reach the entrance to the ITRF's headquarters, Empress Beatrix arrives in her mech with the Claws of Imperium backing her up. As they begin to battle Nya, Sora, and Riyu arrive outside the city on Jiro and Zanth, and briefly discuss the false perfection of Imperium and the fanatic devotion of Sora'sparents.
The Ninja soon discover that Beatrix's mech is impervious to their elemental powers, but Jiro then opens fire on the city's energy barrier using his new armor. It successfully brings down the shield, and the full team of Ninja are reunited as they continue to battle. As the allies exchange info, Jiro communicates with Riyu, who then guides the humans to make their escape while Zanth and Jiro continue to fight Beatrix and the Claws. The humans and Riyu make their way into Imperium's underbelly through an entrance disguised as a dumpster.
Elsewhere, Jordana is attempting to drain power from the Source Dragon confined beneath Imperium but fails in her first effort. The Ninja, passing through the tunnels, discover pieces of the Imperium Monastery thrown away like trash, and Zane realizes that this is why he was unable to reopen the portal gate. Upon reaching the ITRF's headquarters, Percival explains how he and his friends turned against the Empress after seeing the broadcast in which she lied about dragons escaping. They have since learned the truth about the nature of dragons and the fate of Emperor Levo.
Percival and his friends then express their intent to leak footage of the Empress telling the truth about her nefarious activities to the populace with Imperium's broadcast system. While they have an insider to help them access the system, they need someone who can hack the system, and think fate has brought them the perfect candidate: Sora. Having also learned the truth about her and been inspired by her defiance of Beatrix so long ago, the ITRF ask her to help them. Sora agrees, and Arin volunteers to accompany her while Kai and Wyldfyre provide a distraction and the other Ninja go after the Dragon Energy Cores.
Elsewhere, Beatrix defeats Zanth and destroys Jiro's armor, bringing an end to their battle. Lloyd, Nya, and Zane make their way to the lab, and are saved from being spotted by an Imperium Guard due to his recent eye doctor visit. Kai and Wyldfyre blast what is supposed to be the Imperium Armory, only to discover that Wyldfyre's inability to read a map has led them to destroy the Shoulder Pad storage facility. Percival leads Arin, Riyu, and Sora to the broadcast tower, where his insider is revealed to be none other than Rapton of all people.
Riyu is understandably less than thrilled to see their longtime adversary but is persuaded to hear what he has to say. Rapton explains that, where he was only ever interested in hunting dragons, he now sees that Beatrix has gone out of control and is willing to risk ending the world simply to secure her own power. He contacted the resistance, who provided him with the fake energy he delivered to the Empress; however, since escaping from the explosion at the lab, he has learned of her efforts to find a replacement for the missing Dragon Core. He opens access to the system for Sora, who quickly begins working on the system.
As Beatrix intercepts Lloyd's party, Dorama appears at the broadcast tower, having become suspicious of Rapton and followed him. He attacks the group but is knocked out by Riyu, while the Empress mocks the Ninja for daring to think their dragons-whom she has imprisoned-could stop her. Dr. LaRow appears in the Source Dragon's holding room and mocks Jordana, both for failing to drain the Source Dragon and for her obsession with Sora, who is barely aware she exists despite Jordana considering the two of them rivals. In response, Jordana has her dragged away by guards and orders her assistants to proceed without any safety protocols.
Beatrix's fight with the veteran Ninja is interrupted by the broadcast of the resistance's footage, which reveal her actions against her own father and sister and the suffering of the dragons she has used for powers. Many of Imperium's citizens are outraged, and Sora then adds her own face and voice to the broadcast. After denouncing the Empress and her villainy, she calls upon the people to overthrow the Empress, declaring that "We are all dragons!" Angry Imperians descend on the palace and the restrained Jiro and Zanth, even as Kai and Wyldfyre succeed in finding and destroying the actual armory.
Mobbed by her angry former subjects, Beatrix throws aside her own guards and flees, but is then contacted by Jordana. Lord Ras overhears the discord and is pleased, and the guards protecting the lab are called away by the fire at the armory. Unfortunately, just as Lloyd's team reaches the lab, Beatrix appears with her new MergeQuake weapon. She then fires it off and opens a MergeQuake rift, and prepares to turn her new power on the Ninja...
