If a fever is there to raise a body’s temperature to help kill off a virus – why at the later stages of infection does the fever stop being a symptom even though other symptoms are still present? If other symptoms are still present then the host must still carry the pathogen, so surely the fever should last until the host is healthy?
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So a lot of your symptoms are actually your body’s response to fighting the virus. As you said, the fever isn’t the virus, it’s your body’s reaction. It’s the same thing for many, if not all of the other symptoms.
As for why the fever is the first to go, fevers are extremely taxing on the body. They are generally the last line of defense before you suffer lasting damage. Your body will generally “turn off” the fever as soon as it feels the virus is now longer a threat. Some of the other responses require minimal resources from the body and will be allowed to linger.
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