 After the fall of Zebes (Super Metroid), Samus and her crew members travel SR388, only to find more trouble. After the Metroids were consitered to be wiped out, their prey, the more deadlier X-Virus, attacks Samus. So the Galactic Federation surgically removes her armor and injects her with serum from the Metroid Hatching. Now it is up to Samus to rid of the X-Virus and avoid her evil clone on SR388.