So I'm in the process of planning a game where the major city (a port city) is run by a competent leader whose family took over for a king decades ago after the king left town on a routine trip to a neighboring city, but never arrived. So no usurping, just taking over for a missing king.

The story I'm going for is that the previous kings were all pretty horrible, while the new Lords are all very good at running the city. They know this, but they also know that there are people who claim they are usurpers and want the old ruling family back ... mostly the other noble families, who were very prosperous before at the expense of the poorest families. 

The new Lord has quietly had distant relatives of the old king murdered, because he knows that the town was much worse off when the royal family was in charge. What is the blood of a few potential princes/princesses against the starving bellies of thousands in the city?

So the BBEG is going to be a member of the essentially exiled-royal family whose plan is not to take back the city, but to make the new Lord suffer. She wants to punish him for killing several of her siblings and cousins and nephews and aunts, etc. She doesn't want the throne back, she just wants him off the throne. And she first wants to ruin his reputation as a worthy Lord who has brought about prosperity. She doesn't want him to know she exists until her planned time for the reveal -- basically right before she can get close to him to murder him personally. The plan is to have the townspeople turn on him, then when he knows his legacy is destroyed, kill him before he can fix things.

Currently I have that she would be killing/kidnapping any of his messengers as they bring news of his to other cities, to weaken his standing with allies. She's also hiring pirates to shipwreck trading boats and fishing boats in order to reduce imports and resources entering the city. And finally, she's kidnapping and/or killing any city guard that she finds outside of the city in hopes that she can brainwash them (or charm them) into an eventual military coup.

Any other ideas of events that a villain who wants to really choke off a city's prosperity and threaten the Lord stealthily could manufacture? Eventually the idea is for the party to be assigned to do things like escort a merchant ship to another city (only to find pirates attack), or delivering important updates on the city to their allies (getting a few more clues as to the mastermind behind things). Their missions given by the Lord will be to solve some of the issues that the town is facing, only to realize they nearly all stem from the same source.

And then they confront the source and hear her side and move forward one way or other with some degree of moral ambiguity.

How is she going to keep the players from following the threads back to her before she's ready?

To answer your question, though:  Kidnappings.  The fact that she's scrupulously careful that no harm should come to any of her young victims will be your players' reason to stop and ask about her side of the story in the first place, instead of yelling "roll initiative, lady!"

I like it!

And yes, that's going to be the main issue -- the clearly vindictive "princess" who doesn't care about the future of the city, only cares to punish past crimes, versus the well-intentioned Lord who sees the ends as justifying the means.

I'm playing around with the party meeting her beforehand, possibly not realizing who she is. (Part of this is that her forces will be made up of loyalists, some inside the city but most outside, and "evil" races that are mostly just mercenaries for hire. They'll know it is a member of the royal family before they find out exactly who she is, most likely, as defeating some loyalists will result in shouts of "long live the king!" or similar.) Maybe something where she is a "victim" herself and plays at being friendly with the party to learn about them.

This isn't Game of Thrones inspired by any chance, is it? With the Targaryens as the incompetent old dynasty, Robert as the openhanded lord assassinating their descendants, and Daenerys as the vindictive returning princess? The plots are very similar, so if you're not already, try pulling some ideas from there! It sounds like it will make an awesome campaign, especially if it leans into the moral grey.

Edit: it could be that (like Daenerys) the princess is idealistic and sees herself as a liberator, being remorselessly cruel to those in power while giving the people "freedom" that quickly crumbles due to lack of structure. That would show her good intentions, but also her potential for evil.

I had not made the connection at all, actually! (Well, I had kinda compared the last king to some of the worse Targaryens in my head -- part of what he did to ruin the city was simply wall off the poor neighborhoods and say, "You're on your own now!" ... basically the equivalent of drowning all the unhappy guests in Roller Coaster Tycoon in order to say your park only has happy guests in it.)

I think the key difference is that the ruler now is specifically avoiding being a "usurper" ... his family simply took up the mantle when the previous king vanished and have gone mostly unchallenged since, and that the princess doesn't want to be a liberator, she is just straight evil and wants the city to burn if her family cannot rule over it.

Unfortunately, since Dany is in Essos we haven't gotten to see what she would do to undermine the king (I won't acknowledge the last few seasons of GOT, I'm going solely off the books here).

I want to jump back in real quick and say that someone whose family has been mostly murdered by politicians is going to come across as more sympathetic than it sounds like you mean her to.  Didn't anyone think of just abdicating formally?

Quote from TimCurtin >>

I want to jump back in real quick and say that someone whose family has been mostly murdered by politicians is going to come across as more sympathetic than it sounds like you mean her to.  Didn't anyone think of just abdicating formally?

 
That's kinda the point. The Lord is a good leader, but did some abhorrent things to hold onto that power. The previous kings were bad leaders who were variably cruel or indifferent to their subjects.

The BBEG is the same kind of cruel, but it is directed at the Lord only, although that generally means that she's completely indifferent to the suffering she will cause to the rest of the subjects. But she is doing it out of revenge now, justifiably.

The point is that there's some kind of moral question here, though I would say it's not a very difficult one. (I'm also playing up the Lord as being just kinda rude and gross -- think Denethor, but actually a good leader for his people. So the idea is for the party to viscerally dislike him, though he never does anything actively bad to them, and other NPCs have only good things to say about him.)

To be fair to him, book Denethor is a much cooler guy than movie Denethor—he has some of the same flaws, but as I recall, he never tells his troops to give up, and he definitely doesn't crunch tomatoes. Honestly, I could see the characters choosing either side, and I think that's very cool.

You could have the party meet her in a "damsel in distress" situation right at the beginning. Have her request their help to escort her to safety because she is being targeted for death by what she describes as "a jilted lover". She does this to disguise her royal lineage to avoid being turned over to the lord (who the players haven't met yet). Have the players kill a few would-be assassins and save the princess. Then have them travel to this town to meet the lord, who they don't know is the attacker, and have some hints around like recruiting posters for the guard (to replace those the party killed), or the tail of a meeting the lord is having with someone with the lord saying "well, when they do return, send them straight to me!".

Then have the events unfold as you intended, with the party helping the lord to fight this BBEG in the shadows, only to reveal it's the woman they saved at the beginning.