Code Black was a protocol created during the first outbreak, and after the discover of Moon and a few others.

It's also Rainbow's dark secret, because it's run by a team that only Harry and lion are aware of. When the dragons were discovered it was feared they were meat to lower their guard, but also the possibility of other dragons in the outbreak.

Moon was originally meant to be eradicated the minute she was discovered, but Doc protected her. So harry let him keep her to see where it all leads, but at more showed up he decided to have a backup.

He assigned operators to respond to a code black, these ops do not have emotional attachments. If the dragons were to betray or the outbreak become a threat. Harry would call for a code black, which would activate the REACT team that would eradicate all outbreak. This sadly included the dragons, as for the operators that would try to protect them would go into an immediate stasis to prevent it.

-bloodhound-