I'm having trouble figuring out where to start. What could he do first?
Without mods.
Maybe he could root out and kill Dark Brotherhood and Mythic Dawn members, or perhaps just spy on them (so he doesn′t run out of things to do)? Other than that I have a hard time figuring out covert things to do that works in favor of the empire.
I put this in a spoiler, just as a precaution.
I am really sleepy, but let's see if I can think of an Idea or two.
Since the agent will be doing covert missions, this means that you have a lot of work with, mostly imagination.
Is a certain person giving the Empire a bad name?
A certain book seller ruining the Empire's reputation?
A group of Guards that are into illegal trade?
Maybe a whole family that owes the Empire several favors but has refused to pay what's due?
Maybe tasked with the job to spy several people to look for blackmail worthy information?
Are you tasked with stopping the Skooma trade? Or perhaps tasked with secretly distributing it. (Can be done with the duplication glitch) I mean, those sewers in the Imperial City are pretty huge, and you can get into a lot of buildings with it, maybe you're planting evidence.
Hmm, I can think of many other things an Agent can do, but I'm so sleepy. , Will post more ideas when I wake up and get some breathing time.
As Berret says, imagination will play a big part here since there aren′t any "real" quests for this. I like the idea of planting evidence in homes and using the sewers in the Imperial City to go places.
Maybe the empire wants certain items owned by certain people, but those are unwilling to let go of them and therefore you are sent to steal them and bring them to any (or a specific) Legion post? Or maybe you are simply tasked with getting rid of "elements of civil unrest" such as bandits and Conjurers, or perhaps even certain races?
Lots of potential here, I sense