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Picking up from the end of "They Call It Doom", Lloyd and Arin emerge from a portal to find themselves in a strange office structure inhabited by similarly clad agents of various species including humans, Maaray, Merlopians, Munce, and Nindroids. They then come across a line of various people, one of whom explains that they are in "the Administration", the center of all bureaucracy. After hearing a bizarre account of how generations worth of people have stood in this same line, the two Ninja are confronted by a pair of agents, one human and one Serpentine. They ask to see Lloyd and Arin's "permission forms" to be in their current location, and draw their weapons on the pair when Lloyd admits that they don't have any.
In the Wyldness, Wyldfyre worries over Heatwave, whose recovery from his injuries is progressing more slowly than she wants. Kai tries to help her learn some patience by teaching her some calming forms that Master Wu taught her. Back at the Administration, Lloyd and Arin unexpectedly receive permission forms from a pneumatic tube system, pacifying the two aggressive agents. This allows Lloyd and Arin to go off in search of the missing Dragon Core. Unfortunately, the agents then realize that the permission forms lacked photographs per regulations, and instead featured hand drawn pictures of Lloyd and Arin; they thus set out to find the pair.
The same tube system alerts Lloyd and Arin-repeatedly-that the agents are pursuing them, but the agents soon put out a general alert regarding the pair. Following directions from their mysterious benefactor, the pair arrive at a mail sorting cubicle to find it being operated by an imprisoned Zane. Zane explains that, while trying to get the Portal Gate under the Monastery of Spinjitzu to function, the two agents now pursuing Lloyd and Arin emerged from a portal to take him into custody. He goes on to note that the Administration was once part of the Realm of Madness, and that the self-important bureaucracy lacks any real authority.
Zane is able to learn that the Dragon Core has been taken to the demolition level, and that the only way to get to it in time is using giant-sized versions of the mail tubes. They get into one just as the pair of agents arrive, and the agents are able to send them to three separate destinations despite their escape. Lloyd arrives at the demolition level just in time to see a Nindroid piloting a large mech depositing the Dragon Core onto a conveyor belt. Arin, meanwhile, ends up in the Department of Reassignment, where individuals stranded outside of time and space by the Merge are sorted and sent to what should be their home realms-according to the best guesses of the Administration agents.
Arin wonders if the Administration may have found and "reassigned" his parents, but is forced to flee when the agents become suspicious. One of them, Sub-Agent Prentis, promptly calls for his manager, who proves to be none other than the missing Ninja of Lightning, Jay Walker. Jay promptly berates Prentis for bothering him with a matter not related to their department, and then leaves to return to his own "work" of playing video games. On the demolition level, Lloyd seizes control of the mech and grabs the Dragon Core, only to be confronted by a group of agents.
Back in the Wyldness, Heatwave rises, his healing complete, but Kai and Wyldfyre discover that the Dragon Core in their possession is a fake passed to them by Dorama. Zane appears in a strange car to assist Lloyd, and they flee through the Administration facility and are soon joined by Arin. They set out to obtain a punch card that will open a portal for their escape, only for the agents to activate laser grids intended to stop them. While Zane puts his Nindroid skills to use filling out the needed request form for a punch card in triplicate, Arin discovers that the mech is actually two mechs in one and splits the smaller mech off to assist Lloyd.
Zane gets the portal open, and the three Ninja escape through it using their new vehicles, with the portal closing just behind them and preventing the agents from following. They arrive back in the Mother Garden and run into Zant-Tanz, and then board the Destiny's Bounty to depart for home, bidding goodbye to the Mucoids as they do so. Returning to the monastery, they meet a returning Kai and Wyldfyre and learn of the loss of their core. Requiring all three to stop the Merge quakes, the group leaves their core at the monastery and head out in the Bounty to retrieve the core Dorama obtained from Imperium. As Lloyd expresses the hope that this visit will go more smoothly than the last one, a powerful burst of energy is fired off from the city in an apparent signal that it won't.
