Let me start out by saying that I warn against having to many plot-strings in a campaign.
I told my players that not all leads are meant to be followed, but it might be a bit to much with 3 major plots in one campaign, campaign not yet over, so might be okay in the end 
The party consists of 4 brothers of rank 2 now, and one friend still at rank 1.
The plot they're following now is the death (15 years ago) of their mother and their unborn sister, and they've now discovered it revolved around a nurgle ritual to summon the "Virgin of Plague".
The brother who discovered this, did it by finding a book, that seemed harmless ("Life and death of sandworms"), but it was just a front cover, inside it was a book describing the ritual in details. Out from the letters streamed bile, and the character failed his disease check.
Out of all the cards in the whole deck, he drew... "The Plague", quite funny really, but of course the player was not very amused when he discovered just how freakishly deadly diseases are... But I was amused, as the title was "Virgin of Plague" and he drew plague.
Okay, it's been 15 years since the ritual was started, and now their sister has been transformed into the semi-demon "Virgin of Plague", that pretty much insta kills anything that touches her, and gives plague to anyone close to her.
They've tracked her, and here I ended the session. The brother with plague has infected 2 others, so now 3 players have got the plague, and they're looking down upon their sister who's heading for Altdorf.
I decided that, in nurgle's spirit, she's not evil in the normal sense, she's just extremely lonely, and wants to make friends (she constantly cries from loneliness), and so after wiping out an entire village, she can sense the thousands on souls in Altdorf and thus heads there in hope of finding friends.
Okay, my problem is that how does the campaign proceed from here???
There are still one other main plot they're also actively following (the last one they've kinda skipped, which is quite fine really), so even if they solve this one, the campaign still lives on, so no worries there.
So...:
1) I want to play on three of them already having Plague, they should really be immune to her, maybe she says: "You are kindred spirit to me, you should understand me!!!" And in turn they're immune to her touch/presence, maybe...
2) I want to play on them being her brothers, do they have the "power" to calm her down, and maybe understand the wrong in her actions?
3) Can they kill her? (we ended with one of them storming down to her to fire his twin pistols... this one is, btw, not plague infected so won't be immune). Does she just rise again, and what can stop her???
4) This is Warhammer, killing them all is NOT a bad thing!!! But ending the world in one huge plague is bad... Btw, none of them are Shallya priests (one is a Veranna priest...)
5) They really skipped trying to find the person (Doctor Festus) who initiated and performed the ritual, maybe he shows up to truimph, but Nurgle doesn't do that, do they? In a way I see nurgle as a cult that does what do, because they see it as a good deed... The book described the ritual as a good thing, as it would end the worlds constant suffering.
6) If/when she dies, are the characters cured from the plague? Maybe they see that each time they kill her, that their disease (the 3 who has plague) reforms her again? But that seems corny in my mind, a desperate attempt from the GM to cling on to his "adored" npc.
7) I don't like HUGE "show-downs", I actually love it when they kill the main antagonist in 2 rounds, it leaves them slightly baffled. But in turn I let seemingly harmless situations be deadly, like the book, and such. So I don't really want a huge fight where she throws magic around like a mad-woman. Well unless it has a "cinematic" point.
Gah... tough...
