The only thing I remember reading here was that the content of Black Plague was actually supposed to be spread over two episodes, so one scenario I could imagine is that episode 2 would've focused more heavily on a longer search for Dr. Eminiss ([REQUIEM SPOILER]
[/REQUIEM SPOILER]), ending perhaps with Philip finding his father and part 3 being centred around Dr. Swanson and the Tuurngait in more detail.
That's really just a guess though, I don't even know if what I read here is actually the truth.