This might be very off, but if it’s really Merlin who’s stuck in the tree, maybe he can travel the realms like Bran in Game of Thrones, with only his mind? It is established that he is very powerful, so that shouldn’t be very difficult for him. As for the movie theater scene, maybe he was using someone by controlling their mind (kind of a bad guy move) or he just made a projection of himself that spoke to Emma.
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