The last scene?
**S P O I L E R**
In the end we see his mother's book that she painted when she was kid, right? So, we see the monster-tree with his stories drew by his mother since then!!! The tree and his mother knew each other since her childhood!! That means that she send the tree to help him??
And other thing that I wanted to mention... they did really good job in make up department because they managed to make her face lifeless!!! Felicity Jones has a brilliant face, very "alive", you see her eyes and you see a person with so much energy-happy-full of life face and they made her look like lifeless as the character demands... welldone, I was impressed how they succed to hide her happy-energy face!