Something mysterious is going on at the reploid research island. The reploids have ceased functioning, their data strangely erased. The investigation team encounters "irregular" reploids infected with a strange new DNA chip. Known as DNA Soul, it replaces useful data with a devastating Sigma virus and places all reploids in imminent danger. Now it's up to Mega Man X and his comrade Zero to get to the damaged island and find out who is behind the DNA Soul virus. You control Mega Man X, the famed cyborg and Maverick hunter, to battle Mavericks and restore peace. Along the way, pick up valuable DNA Junk to build new weapons, bosses and even a new level.