First off let me establish that I want this discussion to be Safe For Work (SFW).

Let's say you are a mare who is assigned to supervise a being from another world. Later not only do you discover that they are a parasitic being that uses mind control to control their subjects but you are his first host. This being decides to allow you to maintain control of your faculties so long as you don't jeopardize his position and aid him to maintain a foothold in Equestria.

What would you do?

6575833 It's not like you can do anything.

6575833
Well. First of all, if she's been assigned this job, then it stands to reason that either a) her superiors already know how it can mind-control ponies and probably put safeguards in place to stop it flying off the handle, or b) they don't know, and should be informed of that. If the parasite latches on to them, venom-style (changed appearance), or via non-obvious mind-control (no change in appearance), then that means her bosses might ask "hey, I never see the two in the same room together. didn't we pay that mare to look after the alien?"

So either a delicate balancing act of her trying to tell others what's going on without the alien finding out, or is trying to convince everypony into not realizing anything "mind-control-y" is going on at all.

It really depends on the personality of the alien parasite. Like Bad Dragon said, if they're malicious, you can't really do anything.... or can you? Maybe they still need some level of cooperation from her? Like, maybe his mindcontrol isn't flawless? They can move her body and make them say and do what they want most of the time, but she sometimes could make panicked facial expressions and blurt out cries for help for just a few seconds if she really strained against his control. And he knows if others know he's doing this to her against her will, they'll retaliate, and these magical ponies actually might be able to pry him out of her body. So... work together as a team, or risk losing everything. Either that or threaten/blackmail her into compliance.

This being decides to allow you to maintain control of your faculties

That does sound rather condescending. Sort of like if a Goa'uld from Stargate was inconvenienced into getting their host to cooperate with them.

Sounds like the most likely type of friendship between the two would be closer to Stockholm syndrome.

so long as you don't jeopardize his position and aid him to maintain a foothold in Equestria.

What exactly are their goals? I'm guessing they have to do a lot of politicking to establish relations between Equestria and their home world. Maybe bargain for magical resources or something. But building that on deception isn't the best way to achieve things, at least not in Equestrian culture... though I'm guessing they realize that a little too late and by that point they already started deceiving others, so best to keep doing it rather than come clean.

. . .

Now, if his personality isn't that of a stereotypical mind controlling monster, then this becomes more interesting. I'm guessing he has no sense of privacy and that brings its own set of awkwardness with it. What culture does he come from? What are their usual hosts like? Mindless creatures? Then why not pick a random Equestrian animal and control that? Or are ponies the closest to their typical host, and thus they can't? Wait, what if the whole "mind controlling a sentient being" thing is as uncomfortable for the alien as it is for the pony? What, if that's actually a big social taboo on their home world? Something that is seen like slavery is seen by us now (was done centuries ago, but now recognized as abhorrent), or something only criminals do.

Maybe show the alien's perspective as much as the mare's. Write both sides of a situation with their shared body, show the alien having a hard time understanding concepts that would be obvious to us, because of drastic societal/historical differences.