So I'm going to run a game for the first time and one thing I'm planning is for the bbeg to have the person in charge of the city be under his control but I can't find a mechanic that would work for that in game. Any suggestions?

What you are looking for is a monster power akin to the Aboleth's Enslave ability.

Enslave (3/Day). The aboleth targets one creature it can see within 30 feet of it. The target must succeed on a DC 14 Wisdom saving throw or be magically charmed by the aboleth until the aboleth dies or until it is on a different plane of existence from the target. The charmed target is under the aboleth’s control and can’t take reactions, and the aboleth and the target can communicate telepathically with each other over any distance.

Whenever the charmed target takes damage, the target can repeat the saving throw. On a success, the effect ends. No more than once every 24 hours, the target can also repeat the saving throw when it is at least 1 mile away from the aboleth.

That's perfect and the only change I'll have to make is to it's language to add common. Thank you so much 

You also don't need a preexisting ability. "This bad guy can long-term dominate NPCs" is completely legit to do. Long-term domination of PCs is a different thing, and is something to be very careful about.

There’s the Geas spell, though he’d have to renew that every 30 days. 
But there’s the classic non-magical options: Do what I say or I kill your family, that sort of thing. Or BBEG has promised the person they will rule at his side or be his right hand or something. No magic required. And as a bonus, the party can’t simply dispel the effect.

5th level Modify Memory for a more complication-inducing approach.