Something mysterious is going on at the reploid research island. The reploids have ceased functionality... their data strangely erased. Now the investigation team encounters "irregular" reploids infected with a strange new DNA chip. This strange DNA chip, known as "DNA Soul", 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.