There are many conspiracies that have to do with mages. This is mostly because mages are such isolate, scary people that most citizens don't entirely trust, and that the practice of magic is so severely limited. So, people think all types of things- that mages are planning on taking over the government and starting a new order, for example. Or that magic is not actually as limited and dangerous as people are told, and that mages are hiding the secrets of magic from the rest of the world.
The theories are put out, and denied, all the time, but people still believe them, to the point where there are entire organizations devoted to discovering the "secrets" of mages, or saving people from an "imminent" take-over of the government.