Once your body reaches the temperature that it thinks should kill off the germs, you feel hot. You kick off the covers to cool off. If you cool off too much, the chills come back, to keep your temperature high enough to keep the germs from settling in for a long stay.
In addition to making things hot for the germs, a fever also stimulates your immune system, making it more effective.
Of course, when this happens, we grab for some medication to get rid of the fever. This makes us feel better, but studies have shown that lowering your fever can actually make the disease last longer. Of course, high fevers can be dangerous, but a low grade fever can actually be a good thing.