Fall is an important time in bonsai. This is where we direct our trees to do as we please. Fertilization, future cold hardiness, and girth in branches and trunks all come during this time.
Vascular growth is what the tree focuses on in the Fall. This means that producing leaves is not the priority since we aren't going to be photosynthesizing much in Winter. All energy accumulated from the photosynthetic process go to storage in the trees cells. This energy accumulation is what drives the Spring flush of growth. Different species store their energy in different places. Pines are typically in the roots, Junipers are in the foliage, and Deciduous trees are evenly spread in the roots, trunk, and branches.
There is also an important nugget of information about cold hardiness. In bonsai we love the highly ramified branches. In order to get those twiggy branches we reduce the cold hardiness of that branch. The more sugars and starches we have inside the branch of a tree, the lower the freezing temperature is. Therefore, highly ramified branches are highly susceptible to cold damage even though the tree as a whole might be able to withstand a much colder temperature.
Energy management is of supreme importance in the Fall. The more you fertilize the more energy the tree stores. When a tree has a lot of energy it produces long internodes, large leaves, and coarse thick branching. When a tree has a small amount of energy it produces short internodes, smaller leaves, and fine twiggy branching.
This is why following blanket statements about fertilization can be so dangerous. If you just fertilize every 4 weeks with a full dose every year, you're never going to be creating a tree with highly ramified branching and small leaves.
If your tree is wired, this season must be a watchful one for you. Wire bite on the branching of trees most commonly happens in the Fall due to the trees focus on vascular growth. Checking the branches frequently allows you to stay ahead of the trees growth and remove wires before it damages the branch.