You got my interest, but I have several questions and clarifications I'd like to state. Though I understand that crossing over two universes and trying to make all details fit with each other is fairly hard.
I do apologize if I sound like a jerk, I don't mean to. Most of these are gonna be Dishonored though, as I've played it much, and have not played Darksouls yet, but am familiar of their lore.
First question, what happened to the Whalers (Daud's assassin company), are they in hiding? Are they immune to this new plague?
Also what about the seven others, including Daud, Marked (not with the Darksign) by the Outsider? Are they immune too?
What does Piero Joplin say about the Hollows? The last time we saw him, he was working with Sokolov to cure the rat plague and even perhaps the Weepers.
Why is Emily still a child after ten years? In the events of the game, she should be 9 or 10, so now, she should be like 19-20
Are there any other deities aside from the Outsider? What of the four Lord Souls?
And just some corrections: I'm not absolutely sure, but Sokolov actually believes the Outsider exists, the Outsider even said that Sokolov performs weird rituals for him. He just doesn't appear to Sokolov since, in the Outsider's own words: "But if he really wants to see me, he could start by being a bit more interesting." Although, perhaps we could say that Sokolov is just saying that for the record as to not lose his credibility?
Also, the Overseers' religion, the Abbey of the Everyman, is unique in that they only believe in the Void and the Outsider, and believe that the Outsider is evil. They have no other deities included in the religion, no "good" counterpart, so they wouldn't think the disease a punishment, they'd think its just the Outsider doing it for the evulz.
The Outsider did not bring the Rat Plague onto Dunwall, it was actually the Lord Regent. He got the rats, put 'em in the streets to rid it of the poor, but it went out of hand, the rats proved to be too uncontrollable and cleverer than the catchers.
Although, all these can be excused if this is an alternate universe that doesn't follow either Dishonored or Darksouls' canons.