Placing Opposition

In the third series, one of the main antagonists is her own daughter from an alternate timeline where she has become evil and resentful. There weren't a lot of things left in the current world that could challenge her after the shenanigans of the second series.

The key thing to remember as an MC is that you don't get anything for thwarting the protagonists. While it is generally a good idea to make the progression of the chronicle feel somewhat challenging, there is no special benefit to be had by terminating the chronicle early due to failure or character death. When designing opposition for the player characters, the goal should be to maintain the verisimilitude of the world first, and to provide interesting and exciting challenges to the players second. "Defeating" the players is not a meaningful or acceptable goal for the MC to have.

After Sundown has some seriously terrifying stuff in it, but that doesn't mean that the protagonists have to be challenged by it all the time. Indeed, if the players face nothing but enemies scaled to their abilities, the power of the characters won't ever be apparent. A Werewolf on a rampage in war form is a very scary thing, and a couple of police officers are very unlikely to be able to effectively contain it. Having the players periodically overpower challenges of this sort in a casual manner is good for the game. At the same time, if the protagonists never take on enemies that are near their power level, their adventurers will gradually lose interest.

Players should work with the MC to direct their adventurers in a manner where they come into direct conflict with opposition that is in their ecological niche. The MC should take aims to make the world feel like it is persistent and continues to have events and conflicts while the player characters are not around. This means among other things that the powerful elders in the worlds should be available to be communicated with and opposed. But the MC should frankly discuss political and military realities such that players can pick battles they can win. While the choice between two unmarked doors leading to victory or defeat may be fair, it does not feel fair and it doesn't make an interesting story.