While reading the first chapter of the webcomic The Meek, I had a sense of déjà vu, because a number of elements reminded me of a SF novella or short story I had read, years back. (The similarities could just be coincidence, though; there are multiple differences, too.)
I think I read the novella or short story about 15 or 20 years ago. The story was probably written sometime between the late 1960s and early '00s. Most likely the '90s or early '00s. I probably read it either in something like a "Year's Best" collection or in an Analog, The Magazine of F&SF, or Asimov's SF; it's possible however, that it was an issue from decades past, so it could also have been in a magazine like Galaxy.
In the story, set centuries in the future, the main character is a girl in her teens, named, I think, either Leaf or Twig (for the purposes of describing the story, below, I'll assume Leaf). She had grown up orphaned, in isolation from other humans, on a largely forested planet, looked after by "Grandfather", an ancient sentient mind with whom she can communicate telepathically, and who is connected to the trees and other plants of the planet through their roots (and I believe speaks telepathically to all the native lifeforms).
There are human colonists on the planet, but the only other human she is friends with is an adult guy she met who had had a drinking problem. (I think he had promised her he had put that behind him.)
The above is backstory mentioned in various exposition; the narrative takes place over the course of a few days when she is already a teen.
Some colonists, having become aware that the forest world has a controlling mind, want to locate and destroy the root mass nexus that houses Grandfather's consciousness. (Aside: I was reminded a bit of this story when James Cameron's "Avatar" came out, as well.) I don't think Grandfather had done much (if anything) to the colonists; I think their wish to destroy him may have had something to do with the resource extraction permits for the planet having been subject to limitation or revocation if it became provable that the planet has native high intelligence. I think the girl's friend said he would make his way back to the central colony to get an audience with a representative of the interplanetary government to make the case for legal protection, but he fails to make it back to the colony -- Leaf discovers her friend's dead body in the wild, made to look like he had tumbled from some height in a drunken fall.
Leaf encounters somewhere a group of some of the colonists, who say that they or other colonists had already located and were destroying (or were en route to destroy) the root nexus. A woman colonist says something to the effect that they can help put Leaf where she should be, in school with other kids of her age, and pats Leaf's back.
(I don't remember if it was during this encounter or an earlier one with colonists that Leaf defensively slashed one of them with her fingernails, which the story described as razor sharp.)
Devastated, Leaf flees them and rushes through the forest, in the direction to the root nexus mass's location, to see for herself. Unfortunately the woman colonist had slipped a tiny tracking transmitter on Leaf, which Leaf becomes aware of too late. (I think Grandfather may even be the one to tell her that that they placed something on her.) For some reason, Leaf had been unable to sense Grandfather well during her rush, allowing the colonists' ruse enough time to work -- they had tracked her heading and are ahead of her, on their way to burn the root mass that is Grandfather's brain.
Distraught, Leaf hears Grandfather in her mind, speaking of how she will go on to learn wondrous things about the universe after he is gone, and to not despair, because the lifeforms of the planet will need her. As Grandfather's root mass is burned and the story comes to an end, I think Leaf already feels the lifeforms of the planet psychically reaching out for reassurance, which she gives them, telling them she will be there for them.
I did some searching of the Web and Google Books, with various combinations of search terms, to no avail. (One term combination turned up something relevant only in a meta sense, though.)