*Notes: Oh this story is great. I love the way you have given the deer a voice. I read and write a lot of shapeshifter words, and this is right on the edge of that type of story. I have included a line-by-line review below.
Red - changes needed
Blue - suggestions, and comments
***With that, the deer turned and began heading deeper into the woods. Jake stood there, frozen to the spot, his mind telling him to run back to the house, but his body refusing (-ed not -ing) to listen to reason. …
***... It was really just a small outcropping of rock with just enough room for the five of them. (the way this is being said, you are saying there is just enough room for the five deer, but then you have enough room for Jake to enter? He would have been the 6th.) Jake, of course, stumbled in last, falling to the ground and breathing heavily, still wondering why he was even there.
***It was just a few minutes later when he heard a nearly deafening crack and the earth began to roll and sway under him. As the minutes, which seemed like hours, passed he heard more cracks and booms as several tall trees in the woods came crashing down, including one (comma) not ten feet outside of the "cave". When the shaking and nerve-shattering sounds finally stopped, Jake lay still in the dirt until weariness finally overtook him and he slept.