When we exercise we are simply burning energy and the way in which we train determines, to a point, which form of energy we use. By targeting a particular energy system with our training we force our bodies to get better at using that energy which in return promotes appropriate gains (strength, size, cardiovascular etc).
So in simple terms, to get strong we get better and using the creatine phosphate energy system, to get big we get better at using (and storing) the lactate acid energy system and to improve cardio output we get better at using the aerobic energy system. The amount of weight we lift, the number of sets and the rest we take determines this.
This is why part 3 is so important as many people, despite training hard, do not achieve the results their efforts deserve because they do not target the correct energy system.
For example, some one wants to add some shape to their arms and legs so runs on the treadmill 3 times a week for their legs and lift some small weight for 2 sets of 20 reps for their arms. This is not going to challenge energy systems within the arms or legs significantly enough to promote any sort of muscle growth so it is unlikely to result change in shape in the arms and/or legs. The intensity is wrong and this is why it is important to follow the guidelines in part 3.