What causes the body aches that are associated with fever? Is it swelling of joints or flaring of nerves?

Inflammation. Our bodies have many systems that constantly monitor the status. When something unusual is identified, many process commence including increasing the presence of antibodies, fighting white cells, increased blood flow to the area and much, much more. As this problem gets better, the body will turn down the intensity of the reactions via ongoing monitoring. The complexity makes healing easy.