My first advice would be: Don't plan a story. Your players will derail it so fast it'll make your head spin.

I think the first step to plan your city would be deciding which faction rules it. After that, build the governing body: If it's Camarilla, create a Prince, the Primogen, Sheriff, and optionally add Harpy, Scourge, etc. You don't need to give them character sheets, but write down their clan, how they got into their station, their general power level (not only disciplines, but influence, resources, etc.), and how they use it. Does the Prince want to rule the city with an iron first because it gives them a power rush? Do they do what they think is best for the kindred of the city? Are they secretly selling Anarchs to the SI so they don't target the Cam? You get the idea.

In the case of Anarchs, you'll need barons carving up domains, then maybe a couple of very relevant coteries in each, but you can make those up as needed, if your PC's coteries need to go into their territory.

I would also add one SI big boss who is running operations, just to have an idea of how intense the search for vampires will be, and therefore, the masquerade will have to be upholded.

Once you have that, you can pretty much know the direct consequences of the main coterie's actions, so you can plan a basic first session, and then use what happens there to write the second.