Chapter 4You will find this plant in chapter 4 after going upstairs past the letterlock and gaining the Study key in the hidden room.
1.Fill pot with soil
2.Add Sapphire Gloom seed
3.Add water
4.Take plant to the large tree in the lobby area, this is the area we first entered the main building after the fountain at the beginning of the game
5.Place plant in it's spot and the plant will grow and cause the tree to bloom and move it's branches
If you need more help with this you can see my video below: