Further opinions from where I left off:
the angry blackish-yellow sky
Great description. In fact, I love the whole scene with Maggie in the treehouse.
and found she could watch no longer.
I think you should add a "that". It's not incorrect at all, I just think that would make it flow better.
The very desk she could now see Lisa hunched over, tears pouring down her face in a macabre reflection of the outside world she so obviously felt cut off from.
I love the start of this sentence, but the last seven words just feel like they introduce a completely new thought and generally make it ungainly. I'd suggest ending after "outside world".
Those words tore into Maggie’s already conflicting emotions.
I think mentioning "conflicting emotions" in a story is never a good idea. Show them, don't tell.
The note being blown away is nice, though I feel you make it a bit too melodramatic. Don't force the emotions; the fact that it happens is sad enough.
Maggie watched it go sadly,
Again, no need to point it out. The reader realises she's sad.
“I’m sorry, Lisa.” She mumbled
The dialogue should end with a comma, and "she" shouldn't be capitalised.
The scene in Lisa's room is... I'm sorry to say it, but I find it a bit too angsty. We've had a lot of Lisa-angst fics over the years, and it's possible I'm oversensitive. Still, you might want to cut down on the melodrama. It's OK if Lisa is sad and crying, but try not to overdramatise it.
Flicking on her small lamp she frantically searched it,
This looks like she searched the *lamp*. Obviously you mean the desk, but you might want to rephrase it.
for some small shred of comfort.
This is a bit of a cliché.
“Why?” She sobbed
Again, "she" shouldn't be capitalised.
the only other soul on the planet she ever connected to
Should be "she had ever connected to".
I like the note sticking to the mirror.
Her senses of reason screamed in denial of what she was looking at!
OK, you shouldn't have exclamation marks in narrative, so cut that. Also, "her senses of reason" seems a bit wordy. Just "her reason" would do.
I like "vote of confidence".
Some sentence fragments here. One now and then isn't too bad, but things like "Lisa felt as though he was still right here. Silently encouraging her to nurture and cherish the gifts that she was blessed with, not to waste her efforts feeling sorry for herself, she realized." shouldn't have the sentence break.
feeling happiness bloom inside her for what seemed the first time in ages.
Again, mentioning a feeling, instead of trying to illustrate it to the reader. Also, the end of the sentence is a bit of a cliché.
Still good, obviously. (My amount of nitpicks might seem to indicate the contrary, but that's just because I want this to get as good as possible - if I thought it was a "meh" fic, I wouldn't bother so much.) I do find the Lisa scene a bit too melodramatic and angsty, though.
To be continued.