The command code was written into the basic nanites that the ancients first created. This contained a directive that made them attack the Wraith. It also contained a command that allowed the nanites to replicate, so as to "increase their effectiveness", as well as several safeguards: * The nanites could not harm Lanteans. They identified Lanteans by detecting the ATA gene. * They could not alter their own base code. Rodney McKay later allowed them to get around this when he altered their base code to try and remove their programmed hatred.