We need to remove all GDI forces from this area. Unfortunately, the civilians in this area are GDI friendly. You must remain undetected until your base is ready. If either GDI or the civilians discover you, GDI will attack. - Mission briefing
There were many villages in Africa who had suffered at Nod's hands and sided with GDI during the First Tiberium War. Nod would sometimes build its forces in secret without alerting the civilian population to their presence. If GDI caught wind that Nod was in the area they would launch a preemptive strike against them.