I am starting to believe Nimue is the second dark one. I still think it was her in the mask that turned Merlin into a tree as this would go along with Arthurian Legend. Perhaps Vortigan was the first dark one and in order to save Merlin Nimue killed Vortigan with the dagger, thus taking on the darkness to save the one she loved (similar to how Emma took on the darkness to save the town.) I think when Merlin says you destroyed her he is speaking to the darkness, hence why he uses the would destroy and not kill. Merlin can’t bring himself to kill the dark one because he still loves Nimue deeply and is also guilt-ridden as he may blame himself for why Nimue became the dark one. This would also help explain why Nimue can’t kill Merlin and instead turns him into a tree. I know this doesn’t make perfect sense with the whole voicemail thing, but I think that may have just been a red herring.
"To leave an enemy without an answer, say these words to him: Aglaria Pidhol garia Ananus Qepta" and blow in his direction; then he will not know which way he is headed and cannot answer you." - Swedish Trollproverb