We stretch muscles because they are too short and we want to lengthen them. This shortness could be looked at as either structural, lesions in the connective tissue bind up the muscle, or functional, excessive activity from the nervous system creates too many active motor units. In reality of course there is generally a combination of both and the two affect each other but for now it's sufficient to know that we're trying to overcome one or both of these limitations. The studies of connective tissue and proprioception respectively (coming soon) will give you more information about how this happens.
The nervous system is a quick acting regulator, this means that if we do an exercise and immediately notice a change in muscle length it's been through the immediate action of the nervous system. Changes in connective tissue length will take much longer.
As we've already seen the collagen fibres in the myofascia tend to be arranged in the direction of the force applied to them. When localised adhesions in the connective tissue, through scarring or overuse, cause matting of the fibers, the capacity of the muscle to stretch out is reduced. Prolonged tension in one direction, such as that produced during stretching, will encourage new collagen fibres to follow the direction of the stretch.
A quick stretch will create a myotatic (or stretch) reflex that causes the muscle to contract. Slow prolonged stretching is thought to override the myotatic reflex and eventually reprogram it to allow for a lower level of motor activity in the muscle. Some stretching techniques, such as the active techniques described later on, take advantage of the neuromuscular interactions to increase muscle length.
Stretching is obviously a good thing to do but it can do more harm than good if not done properly.