Anyone can light a bush on fire and speak from it or around it. I don’t think we are alone, but even a human being could do that.
Also, it’s possible for a staff to turn into a serpent, but you simply remove the staff and replace it with a snake, in slow motion you could see the staff going away and the snake appearing. from our perspective the universe would have “appeared out of thin air”, so if there were things living in that world that it came from they could most certainly be able to take things out and put things in. From our perspective though it would appear as if things were appearing and disappearing.
Changing water into wine, same thing, you take out the water and replace it with wine, simple.
Walking on water, suspend the person on top of the water giving the idea that you are walking on water, provided there were “spirits” this would be simple for them, but something would be holding them up.
stopping the storm, what did he do, wave his hand or something and the storm stopped, all that it would take is an understanding of the weather and affecting it in such a way the storm would stop, adding or removing an ingredient to make it stop, he could have had help in doing so.
I think that “miracles” can be real, but would still have a scientific explanation, i also think that the world of spirits can be real but would also have a scientific explanation and understanding.