Board Thread:Lore Discussion/@comment-13436964-20130726062712/@comment-24755309-20151012192702

Ironically, he was assassinated, but not for that reason as you pointed out.

But, looking at the Agent's personality, he was probably tired of being spit on by the people above him, and probably wanted to have his revenge by taking over the Empire, getting to the top, and then spitting on those same nobles who had spat on him before.

It seems that, like the Dragonborn, he became corrupt and only really wanted power for hisself.