What Happens To You When You Run?
When you go for a run, you are ripping and tearing the fibers in your muscles.
The act of working out refers to the process of damaging your body so that you can temporarily make it weaker.
Once your body has been weakened, it will do its very best to repair that damage. Your body is very reactionary; whatever the latest stress that has been put upon it is assumed to be the sort of stress that is going to be put upon it again in the future.
By rebuilding the muscles and repairing the tears that you inflicted on them, your muscles are adapted to the workouts that you have been performing. The next time that you run or bike or swim, your muscles are going to have better protection from that activity and the workout will seem easier.
As you perform similar workouts over a period of time, your body becomes better at dealing with the strain.
The entire idea behind creating a workout calendar or schedule is to best utilize the small improvements over a period of time to see large gains at a specific point in time.
When your body repairs your muscles and improves them, the muscles tend to become a little larger or a little denser at the same time as they become a little stronger. This is problematic, because muscle tissue is metabolically expensive. In other words, it takes more calories to maintain muscle mass than it does to maintain fat in your body.
Because muscle mass is expensive, your body wants to break down any excess muscle that it does not believe is being used or is necessary for survival. If you are not keep performing the motions and activities that cause your body to create muscle, then your body will break that muscle down and cause it to go away.
So now you have a (very) basic understanding of how muscle is affected by exercise and lack of exercise. Working out damages your muscles so that they can grow back bigger and stronger, and resting can break down your muscles so that your body does not have to work as hard to maintain them.