I would say that the "first" Hermione picked the stone up from the ground somewhere. The stone might seem to be in a loop, but I think that we just see one possibility, one universe, where all went according to plan. There must be several instances where she didn't make it in time, didn't hit herself with the stone and so forth. But what do I know.. Just because I read the book over 20 times, it doesn't make me an expert on time travel.. 
When I was young, there was a god with infinite power protecting me. Is there anyone else who felt that way? And was sure about it? but the first time I fell in love, I was thrown down - or maybe I broke free - and I bade farewell to God and became human. Now I don't have God's protection, and I walk on the ground without wings, but I don't regret this hardship. I want to live as a person. -Arina Tanemura
