I'm quite sure it's the viscount's evildoings... Poor Emma pretty much disappeared from this volume, just like that! But I don't know, wouldn't it make more sense for the bad guys to just kill her off? I mean, it's not like in this time period police would be able to find them by their DNA or whatever... Oh well, for the sake of the story they wouldn't be able to do it anyway I guess lol.
I feel bad for Eleanor too, she didn't deserve any of it, such a sweet girl ;_; Hope she'll get over William and find her own happiness soon enough...