As noted, there are spoilers here. And a really dickish bug.
On act 2, when you're collecting your source, if you elect to kill everyone instead of getting the source points, Malady acts as a sort of a back door to completing Act 2. This causes her to die a the beginning of Act 4.
However, if you get all the source ticks, and then complete all the possible quests in Act 2 that give source WITHOUT going back the Miester, the game treats it as though you'd failed (even though you just haven't talked to the Meister to finish it up) causing Malady to end up getting killed some 10-15 hours later. This is triggered the instant that you finish the last quest, so even if you talk to the Miester before talking to Malady she doesn't recognize the quest was completed.
Pretty ticked off about this, as I don't really feel like completely redoing 1/2 of chapter 2 and all of chapter 3.