Board Thread:General Discussion/@comment-26311512-20150512071859/@comment-24674051-20150512150045

ChocolatEyes613 wrote: While Merlin is the main contender for Lily's father, I still have one question.... why would he let Issac and the Charmings corrupt his daughter?

PS: I prefer the "Lily's father is Arthur Pendragon" theory better.... she would still have a connection to Merlin. Maybe because he sees the bigger picture?

Consider that the Sorcerer apparently sees the future, and sees it clearly (unlike Rumple). He knows that Lily and Emma's fates are linked, and that they were linked even before the debacle with Isaac and the Charmings. What if Emma and Lily are both a part of his plan to ultimately defeat the Dark One. Consider:

Emma - Born without Dark Potential. Possesser of the strongest light magic. Probably 'bred' (I don't like that word here) to be the ideal vessel to contain the Dark One.

Lily - her purpose was to absorb Emma's initial dark potential. Lily probably has a strong light magic inside as well (not to mention the dragon ability), in order to counter the full effect of darkness. and it would make sense that the light in Lily comes from a strong source of light, namely Merlin.

So they journey together, and when they meet Merlin, Merlin seperates the Dark One from Emma, and then restores the "normal" Darkness from Lily to Emma. Emma, after surviving the tethering to the DO, is easily able to manage the darkness from her own potential, and with the lifting of the darkness from Lily, both become powerful light sorceresses, and their power, combined with Merlin, is finally enough to deal with the Dark One permanently.

Just a theory.