The Empire's Congress
Unlike most empires, the Eln Empire is actually headed by a congress. Although there is an actual Emperor he is merely a figurehead. The Congress is made up of bankers and military commanders. With their combined knowledge they have managed to bring the Empire to the world power it is today.
The Congress as well as the Emperor were killed when Ret destroyed the palace. Farnui had just been inducted into the congress prior to its destruction. He was one of the small handful of members who were not present at the palace when it was destroyed. In the confusion following the destruction of the palace and congress all the other congress members died or disappeared mysteriously allowing Farnui to easily find his way into power.