Microbes and oxygen, mostly. If an apple falls and its skin breaks, oxygen in the air will turn the apple brown. Tiny microbes also eat the apples, especially where the skin is broken. It takes energy to keep things healthy and whole, and the apple is not getting energy from its tree after it falls, or even when it is ready to fall.

Fungi infect apples and digest them from the inside. This is what we call "rot" - the apple getting eaten by fungi.

Bruising or browning of an apple does not mean that the apple is rotting. The most common reason that apples rot is due to fungi and molds that use the apple for food to grow. If an apple becomes bruised or punctured it can expose the apple’s interior to fungi. The fungi release molecules known as enzymes that break apart the apple cell tissue to expose the apple’s nutrients, and the fungi uses these nutrients to grow.

Keeping apples in a cool, dry environment can help prevent rotting because fungi and mold usually grow in a warm and humid environment.