To the west of Nekhen and located some 500 meters inside the wadi opposite the city, stands the mud-brick structure known as "The Fort". This structure has been dated to the reign of the 2nd Dynasty Pharaoh, Khasekhemwy, due to the excavation of fragments of a granite doorway inscribed with the Pharaoh's name and has lead to the speculation that it was constructed for the Pharaoh's funerary cult. The Fort is similiar in construction to the structure located at Abedjou known as Shunet el-Zebib, which is also ascribed to the Pharaoh Khasekhemwy; however, the Fort is only one third of the size of Shunet el-Zebib. Despite the thousands of years that has passed since its construction, several portions of the walls rise to their full height and proudly claim the distinction as the oldest mud-brick building in Egypt.

Directly surrounding the Fort is evidence of Predynastic settlements and cemeteries reflecting the very early origins of the area. Included among the Predynastic tombs is the famous "Decorated Tomb 100", now unfortunately lost. This tomb was found in the easternmost portion of the settlement/cemetery area at the closing of the 19th century. It was constructed with mud-brick and its west wall was decorated with a remarkable painting depicting boats, animals and men. The simplest burials of the Fort Cemetery would have been without any coffin and only a few grave goods, usually pottery and some beads. Higher status burials were larger and slightly more elaborate, the tombs sometimes being lined with wood or mud-brick and provided with roofs. Grave goods within these burials were of a greater variety and quantity, suitable to the status of the dead. The Fort and its surrounding cemeteries are not strictly confined to the Predynastic period however, close by are decorated and inscribed rock-cut tombs ranging from the 6th to the 18th Dynasties.

Copy of painting from Decorated Tomb 100

The Fort and its surrounding cemeteries would have been a place of veneration, a place to honor the ancestors of your family and honor the ancient chieftains of Upper Egypt. Funerary cults would have flourished, some administered by priests, others administered by the families - depending upon the status of the dead. The nearby Predynastic settlement would have been home to the earliest settlers, those carving out a home close to the Nile and forging the communities that would give birth to the Egyptian cities. The settlement would have been overseen by a local chieftain, usually given the title of Great Chief, who held the responsibility of the well being of his people. The Great Chief would have been responsible for most aspects of village life, ensuring there was enough food, protecting the settlement and engaging in diplomatic exchanges and trade with neighboring chieftains. In time these Great Chiefs became the earliest kings of Upper Egypt, building cities, expanding industry and eventually even uniting the land.