Mary Sue Factories are installations which create Mary Sues in vast arrays of pods filled with hyperenergetic fluid. The various Factories are run by a Flower Administrator. The rest of the staff are composed of other Flowers, and Defectives, with the exception of the FGenMS01 following the Reorganisation, which utilised fully-functional units rather than Defectives.
The FGenMS01 Mary Sue Factory was the original prototype Mary Sue Factory, set up by the Mysterious Somebody early in his reign as a source of funding for the PPC. It worked so well that he decided no more were needed. No one was inclined to question the sudden prosperity at the PPC, and so the Factory, run by the Orchid, went unnoticed for seven years.
In 1998 HST, Agents Blue Photon and Tango Dioxide of the Department of Mary Sues stumbled upon the Factory by chance. Blue told his girlfriend, Imbolc Telyan, who told the Evermind; the Evermind found more details, but was killed before she could reveal the information, and Blue was imprisoned.
In 1999, the Orchid and the Nightshade attempted to destroy the Factory, but had to flee with the job incomplete. These events rapidly grew into the event known as the Reorganisation. Due to the actions of Nyx Nightingale, the Mysterious Somebody was driven out of HQ, and took over control of the Factory, with the Bindweed, Gladiolus and Marigold serving him.
In 2006, the Mysterious Somebody led an army from the Factory into HQ. This army inflicted severe casualties on both the PPC and Black Cats, nearly destroying the Disturbing Acts of Violence Department and Parma Division, but was itself wiped out when the Mysterious Somebody died. The Factory was also destroyed in this crisis, killing the Bindweed with it.
Following his exile from the PPC, the Mysterious Somebody set up, or caused to be set up, several other Mary Sue Factories. After his death and the destruction of the original Factory, they became independent, but have now formed a League of Mary Sue Factories which is once again threatening HQ.
Agent Eledhwen Elerossiel is said to have been taken prisoner in one of the League's factories. She escaped to HQ with the news of said Factory. The Factory in question is said to have performed cloning experiments on her, resulting in a Suvian counterpart of Eledhwen.