The black flag directive was a type of order used by Starfleet for committing an action, making it appear that it was the work of another entity, and then concealing the evidence that it was Starfleet which did the action.
In the USS Ibn Majid incident of 2390, Captain Alonzo Vandermeer received this directive straight from Starfleet Security, informing him that he had to murder the ambassador Beautiful Flower and his young protégé Jana, or his ship and crew would be destroyed. The captain complied, then subsequently killed himself. His first officer, Commander Cristóbal Rios, in accordance with the directive, attempted to cover up the murders by transporting the bodies into space and deleting the transporter log. All information on the ship was later classified. (PIC: "Broken Pieces")