You dont have to vaccinate every man, woman and child in the country if you have a couple of cases of smallpox cropping up.
You can have an epidemic in a state. You can have it in a region. You can have it in a country where the critical level of disease passes a certain threshold and we call that an epidemic threshold.
Previous efforts to eradicate malaria failed for several reasons, including political instability and technical challenges in delivering resources, especially in certain countries in Africa.