To be fair, a large portion of it will become urine, because apples (and apple sauce) are high in sugars. These will be broken down by enzymes in your stomach/gut and absorbed into the body, and will be used in respiration and power your cells as energy.
The remains of the broken down sugar will exit from your cells into your blood stream again, where it will then form urea once it reaches the kidneys as part of your metabolic process, and it will carry on to your bladder, where it will eventually be excreted as urine.
What can't be broken down and absorbed, such as the cellulose that makes up the plant cells in the apple, and other fibre, will pass through your digestive tract. Most water and other nutrients will be absorbed, and the remains will be excreted as poo.
Some water may be excreted through your skin as sweat, or your mouth as breathe.
This happens with pretty much everything you eat.