Let’s look at an example first.
Say you are overweight, so you decide to lose weight.
You cut down your food eating, take in 1800 calories a day and to burn 2200 calories per day. Now your total calorie intake is -400 cals.
So, where does your body get the 400 calories? The answer is – fat in your body.
When you eat less calorie than you burn, your body will get the energy from your fat cell. Then your fat cell size will be smaller, this is how you lose fat and become slim.
In fact, the fat burning process is more complicated, but the above thing is enough for the question.
The fat is used to fuel your body, that is where the lost fat go.