The best explanation for the ache and fatigue in the runner's muscles is that his/her muscles have accumulated lactic acid due to anaerobic respiration taking place in the muscle cells. When the muscles are involved in intense exercise, they don't have enough oxygen for the exercise they're doing, so anaerobic respiration takes place- that is, they have to break down carbohydrates into something called lactic acid, which increases the acidity of the muscles and makes them sore.
