[quote=Schradinger]
It was either that or have him start being manipulated behind the scenes by someone else in the empire, perhaps a powerful Mage or the leader of the Penitus Oculatus. Then after a bit have another figure rise to prominence, expose the plot, and replace the current emperor. It just doesn't feel right to kill off an emperor without some sort of intrigue.
[/quote]

That's a possibility as well. Cyrodiilic emperors get assassinated all the time, not matter if they are Remans, Potentates or Septims, no monarch's safe from sudden death.

You have the freedom to choose whatever you want in this situation, just make sure you state it explicitly in your NS.