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As Lloyd and his students bring Nya and Kai up to speed on what's taken place since their last encounter, Sora remains convinced that Riyu is the source of her Tech powers and not merely an amplifier. Their journey on the Destiny's Bounty is interrupted when they arrive at the Cloud Kingdom. Suddenly, a Merge quake occurs, and from the rift emerges a monstrous tentacled creature that begins attacking the city. A pair of Ice Dragons who have recently taken up residence in the Cloud Kingdom engage the creature, and Sora soon leaps in using her newly repaired mech.
Much to Sora's astonishment, a group of citizens continue their work of writing on scrolls as the attack is ongoing. The Ninja then hit upon the idea to drive the creature back towards the rift from which it emerged and close it, hoping that the creature will be drawn back into the rift in reality. Arin and Sora, knocked from the city by the battle, are unexpectedly saved by Wind, which proves to have been manipulated by one of the monks. The Ninja drive the beast back into the rift and close it, but it soon begins to reopen without their knowledge.
After discussing the apparent increase in Merge quake frequency and spread, the Ninja approach the monks, one of whom introduces himself as Suetonius, the current Master Writer. The veteran Ninja are quickly reminded of monks' belief that their writings control destiny, though Lloyd is quick to note that the "Writers of Destiny" also tend to ignore when destiny defies their wishes. However, Nya sees the potential to find some answers about the Merge in the Cloud Kingdom's archives, and a monk named Marcus leads the older Ninja off while Arin and Sora remain on watch. Sora continues to doubt her powers and resolves not to use them again; while comforting her, Arin spots the monk who saved them earlier.
The two follow their rescuer and confront her about their knowledge; she refutes their claim, however, as the Writers of Destiny believe in not becoming involved in action. unbeknownst to them, they are being observed by Rapton and his fellow Claws of Imperium. Meanwhile, the older Ninja find their search disrupted when the worms that sort through information in the archives suddenly begin to attack them after seeking information about halting the Merge quakes. The rift from before opens wide enough for the monster to reemerge and continue attacking, in defiance of Suetonius' assertion that their writing would prevent such an outcome.
Unable to reach the older Ninja, Arin goes looking for them only to be caught up in their battle with the worms. Sora, meanwhile, attempts to get her mech working without using her powers, despite Riyu's offer of help. Euphrasia, the new Master of Wind, sees the futility of Suetonius' denial and fights to protect her home. When two more creatures emerge from the rift, Sora goes back on her own resolution and powers up in order to pilot her mech against the beasts.
The other Ninja, having been rescued by Arin, appear to join the battle as well, and together the new and veteran heroes succeed in forcing the beasts back into the rift and closing it-this time permanently. Euphrasia then approaches Suetonius, expecting to be exiled for taking action instead of observing as the Cloud Kingdom's beliefs have always demanded. However, Suetonius has seen enough to convince him that the Merge, if nothing else, is outside their control, and asks Euphrasia to help him reevaluate the way they do things. Marcus, meanwhile, speculates that someone may have cursed the Scroll-Worms to attack anyone who sought specific information, though he is unaware who would be capable of such an act.
Still eager to find answers, Nya decides to remain behind in the Cloud Kingdom to search the archives manually while Kai, Lloyd, and the others return home. Sora decides that she will have to find a way to master her powers, as they seem necessary to the ongoing conflict. Unbeknownst to the heroes, Rapton has captured the two Ice Dragons, having taken advantage of the ongoing chaos on the orders of Empress Beatrix and Lord Ras.
