After further thinking about this prophecy, I've got 3 theories. Banking on the last one:
A. The villain under the hood is Regina/The Evil Queen. She is the only person missing in the vision and it has always been destined that these two women will go head to head. Regina has been chasing Emma since birth and Rumple even said once that there would be a great final battle.
B.The villain under the hood is Emma herself. Here Emma thinks she is going to die and not have a happy ending but all together Emma is keeping herself from having the happy ending. It might be revealed that it is herself.
**C. The damn prophecy is staged to get inside Emma's head and it is a plan by Jafar who was brought over with the untold stories. If you notice she has to follow a "red bird" that would lead her to the "Oracle". Well I believe that "red bird" was Iago from Aladdin who was also a red bird. And that bird led her to the "Oracle" who I believe was Jafar in disguise. If you notice the girl she was speaking with carried something that looked very similar to his serpent staff.