A couple of days ago I reheard some of Amaund Mortierre's dialogue and suddenly made a connection. He talks about how the Emperor of Tamriel had to be assassinated in the earliest periods of the Septim Dynasty to ensure its survival, or something to that effect, by changing the political landscape and he goes on to say that the same has to happen now. Most people, including myself up until recently, saw this as a generally good thing, but then I made the connection to some of Tullius' dialogue regarding the Emperor:

"Most of the Legion is tied down on the border with the Aldmeri Dominion. The Emperor can't afford to risk weakening Cyrodiil's defenses. From the Imperial City, our war here is just a sideshow. An interlude before the main event against the Thalmor resumes."

If Mortierre wants to change the policy of the Empire, how does that relate to what Tullius says about the Emperor preparing for war with the Dominion?

Heck, Motierre probably works for the Thalmor.

You do know he isn't dead right?

http://m.youtube.com/watch?v=8lXdyD2Yzls

Yes, I lean towards that being the most likely scenario, considering that you see two different Mortierres during the Dark Brotherhood.