So I have a theory on the Tree of Harmony(TOH). The theory is that the TOH won't last without the Elements of Harmony(EOH). I think that those roots/whatever they are got into the tree because the EOH weren't there. I also think that the smoke that took over Nightmare Moon came from that tree. For a second, you might think that doesn't make sense. But I also have a thought that the Shadow Pony came out of tree before it got destoryed and then it is now trying to destory the TOH again.