Step 1 :The function \(N(t)=\frac{12,000}{1+999 e^{-t}}\) models the number of people in a small town who have caught the flu \(t\) weeks after the initial outbreak.
Step 2 :To find out how many people were ill initially, we substitute \(t=0\) into the function \(N(t)\).
Step 3 :Calculate the number of people who were ill initially and round the result to the nearest person.
Step 4 :The initial number of people who were ill is \(\boxed{12}\).