An obligation to protect civilians has become a standard part of the mandates for UN peacekeeping operations – often in difficult and volatile situations with many actors. But relations between host governments and UN missions are complex. Question arising include sovereignty, trust, respect, intercultural communication, and control. Outside interventions can be resented as interference, Security Sector Reform may be unwelcome, and agendas may be very different. The government of a state still has a primary role in protecting its own citizens, even if it is part of the problem. This paper explores some aspects of the relationship, which can effect whether a mandate to protect civilians can be implemented. It draws on the experience of South Sudan in particular.