thank you for the reply. the spots are dark brown and when took to the doctor they did nothing but gave a syphlis test which was neg.
Dark spots underneath the skin on the bottom of your foot can be signs of a blood-clotting disorder called purpura.
If you bruise easily ( anywhere on your body ) and the spots ( on your feet) are red or purple please see a doctor as soon as you can.
Because you are saying that there is fever, throat and muscle aches involved, it would be in your best interest to see a doctor as soon as you can.
Are the dark spots more like little holes?
If so, then it could be a type of wart. Warts thrive in wet, dark places...such as the bottom of your feet.
It could also be a type of fungal growth as well.