The Reorganisation is the name given to the series of events which led to the ousting of the Mysterious Somebody from the leadership of the PPC, the destruction of the Department of Internal Security, the formation of the Board of Department Heads, and the extremely small budgets of the PPC.
The Reorganisation is chronicled here.
The Reorganisation starts when Agents Blue Photon and Tango Dioxide find the Sue Factory, a PPC-run facility that produces Mary-Sues. Blue then tells his girlfriend Imbolc Telyan and she informs the Evermind, who was then head of the Department of Finance, about the corruption in the PPC.
However, the Evermind is killed by the DIS before she can do anything, and Blue and Tango are blamed for it. The DIS tortures them and Tango agrees not to talk about what she saw. Blue, on the other hand, refuses to give in, as Imbolc may be endangered. He is imprisoned in the DIS cells, and Tango is reassigned to the Disturbing Acts of Violence Department.
Ontic Laison, a thoroughly insane agent in the DIS, deceives Imbolc into thinking that she is her friend. However, when Imbolc voices her opinions to the Sunflower Official, Ontic lures her into a quiet corner of HQ and murders her with a knife. In the meantime, Tango tries to tell all she knew to Carreg Sarna, a fellow member of DAVD, who has been assigned by the DIS to keep an eye on her.
On hearing that Tango has broken the terms of her freedom, the DIS, through Ontic, orders Carreg to poison Tango's Bleepka. Another DAVD agent, Echo, drinks it and dies instead; in revenge, Tango kills Carreg and flees HQ.
Meanwhile, the Sunflower Official ponders Imbolc's words, and decides to act. He sends his trusted agent, Nyx Nightingale, to the DIS to investigate the rumours about Carreg's death. When Nyx reaches DIS Central, she is "accidentally" transfered to the infamous department. She is introduced to her future companion, Dassie Hyrax.
The Sunflower Official tries to visit Blue's cell, and meets Nyx. After promising to get his agent out of the DIS, he then visits Blue and is told about the Sue Factory. A short time later, Dassie and Nyx arrest Agent Palaver, an assassin, on fraudulent charges.
Nyx talks with Dassie and finds out how the DIS steals competent people from other departments and turns them into cold-hearted killers who have no respect for the lives of other people. When Dassie expresses his hatred for the Bracket Fungus, Twp'atwt, an anthropomorphic Pine Marten who is one of the top agents of the DIS, blackmails him into infiltrating the Mysterious Somebody's office and find out who the head of the PPC actually is. Dassie does so, and is subjected to mind control.
The Sunflower Official, after mulling over Blue's words, calls a meeting of currently partnerless agents. After telling them of his suspicions, he then sends them to find the Sue Factory.
Just a while later, the Nightshade finally convinces the Orchid to act against the Mysterious Somebody, and an "accident" is caused in the Factory.
Dassie is returned to DIS Central, and seemingly becomes a cold-blooded killer. When Mara Jade is temporarily brought to Medical after a really bad fic, he remembers everything about his stay with the MS. After he tries to tell Nyx the true nature of the head of the PPC, the mind control resumes and he goes back to Mysterious Somebody's lair.
In his lair, the Mysterious Somebody tortures Dassie and takes a few samples of his blood for an as-yet unknown purpose.
The Orchid and the Nightshade bluff Twp'atwt into giving them more time, and then flee. Nyx tries to tell the SO about the MS, but she doesn't convince him. In a last-ditch resort, she brings Luke Skywalker to HQ so that his presence may turn back Dassie's mind control, and brings the agent to the SO's office. There, they convince the Sunflower that the Mysterious Somebody is evil, and the SO gathers his allies and evicts the Mysterious Somebody and many of his supporters — including the Bindweed from Finance and the Gladiolus, Head of the Department of Bad Slash — from their posts. However, the DIS is retained.
The Guards try to keep harassing the other departments — and attempt to murder Dassie, now in Medical, and Nyx. Agents Jared Calinson and Jay Thorntree lead a revolt against the DIS in the corridors of HQ. Soon after, the Bracket Fungus sends Ontic, Twp'atwt, and Nendil Morifëa to assassinate the SO.
The SO survives (thanks to Nyx's help), and declares war on the DIS. Blood flows through HQ, and Daleks brought in by the DIS surge through the halls. But thanks to the heroism of Agents Mortic Wentway and Jay Thorntree, the SO's forces prevail and the DIS is driven out of HQ.
The SO reorganises the PPC (hence the name of the chronicle), and creates the Board of Department Heads. He also splits the former functions of the DIS among the newly formed DES, DIA, and DIO. The Clover becomes the new head of Finance, and the Tomb of the Unknown PPC Agent is built on the site of the former DIS Central.