So there is the Emperor then.
I still do doubt that it is the Emperor Marcus does mention in his speech. It seems Marcus isn't really loyal to Empire, else he wouldn't act sorry for fighting back and killing you instead. Another thing we shouldn't forget that technically, Marcus isn't our goal, our goal is Inhibitor that he is defending, yet we are told to get rid of him. In other words, at some point, we are forced to do certain things, which pretty much means there's someone standing behind us, and we pretty much will do things in the Name of our Master.