When you keep to much ATP in your body your body temperature rises high could that be a reason for flu and the medication counteracts it?

No such thing. interesting ideas, but I suspect you have misunderstood something you learned in school or saw online. There is no such thing as "too much ATP in the body". If there were, it would not cause fever or elevated body temperature, would not increase susceptibility to influenza or any other infection, and would have no effect on medication for flu or anything else. Best wishes.