What about a shadowy organization the MC learns about and focuses on that just wants to be left alone or even do good things that those in power would oppose. An example might be to help spread religious freedom, or to end the slavery of beast-kin.y
By the MC focusing on them, they not only are distracted away from the actual Evil people but may actually harm innocent people, or worse, those doing good.
There are many cases where shadow organizations were not evil and were hunted. The Illuminati was actually the name of a group in France during the renaissance that focused on spreading learning and encouraging it.
When Homosexuality was illegal, they actually created a loose community with their own gathering places and passwords to enter. All they wanted was to be able to be who they were.
The Underground Railroad was used to help slaves escape
Now imagine all of them in a city or country that was under the sway of a theocracy that controlled learning, despised homosexuality, and allowed slavery of non-humans