Trauma is often a cause for foot pain. It sounds as if you are describing a case of metatarsalgia – a general diagnosis that describes pain in the metatarsal region of the foot (the ball of the foot). Pain is often described as sharp or aching/burning. There are many causes of metatarsalgia but your history of the pain starting after stepping on a rock makes a cyst one of the more likely causes. If you do end up having a cyst, it may be treated with cortisol injections, or it can either be drained or excised.
The best method of evaluating your foot pain is to visit your primary care physician or a podiatrist to perform a physical exam and possibly an x-ray. That way, the exact diagnosis may be made and the appropriate treamtent employed.