A low-to-medium level Wizard is the brains and the actual Evil Guy, advising a foolish noble who isn't really aware of everything that's going on. The noble can be both the final boss fight AND the way for the players to use the existing organization for good.

Also, make them a gnome and a half-elf and call the gnome Brain, and have the half-elf always ask him what they are going to do next. "Hey Brain, what are we going to do tomorrow night?"