In ancient times, long before the Galactic Empire, the Sith had had another empire that had spanned much of the galaxy. After the collapse of that organization, it took many years before their successors, eternally hidden to avoid attracting the attention of the Jedi, were revealed again to the galaxy. Darth Maul's unexpected appearance on Tatooine awakened the Jedi from their illusion. And if the Rule of Two was still valid for the Sith, surely where there was an apprentice, there must be a master somewhere.
Maul, Dooku, and others were nothing more than pawns for that master, Darth Sidious, who, unbeknownst to anyone, had set in motion a plan that would end up causing the almost complete destruction of the Jedi Order.