Short answers, pulled from the story.
Prehistoric Egypt was the period from the first human occupation of the region to the start of the First Dynasty of Egypt around 3100 BC. The Predynastic phase is traditionally defined as running from the final part of the Neolithic, beginning about 6210 BC, to the end of the Naqada III period around 3000 BC.
Most Predynastic finds come from Upper Egypt because the silt of the Nile was deposited more heavily at the Delta region in the north. That silt completely buried most Delta sites long before modern times, leaving the southern, drier sites far better preserved.
Archaeologist Waldemar Chmielewski found some of the oldest known structures near Wadi Halfa, Sudan, at the Arkin 8 site, which he dated to 100,000 BC. They survive as oval depressions about 30 cm deep and 2 by 1 meters across, many lined with sandstone slabs that supported portable dome-like shelters.
Sequence dating is a system developed by WMF Petrie to establish the relative date of a Predynastic site by examining its pottery. It was needed because all absolute dates for the Predynastic period are tenuous, and it tracks features such as blacktop-ware and the shift of pottery handles from functional to ornamental.
The Naqada culture spans Chalcolithic Predynastic Egypt from about 4000 to 3000 BC and is divided into Naqada I, the Amratian, from about 4000 to 3500 BC, Naqada II, the Gerzean, from about 3500 to 3200 BC, and Naqada III, the Protodynastic period, from about 3200 to 3000 BC. During Naqada II cities grew as large as 5,000 and mud bricks were mass-produced, and during Naqada III Egypt was unified.
The 2025 study sequenced the whole genome of an Old Kingdom adult male from Nuwayrat, radiocarbon-dated to 2855 to 2570 BCE, who had been buried intact in a clay pot inside a cliff tomb. Most of his genome was associated with North African Neolithic ancestry, while about 20% could be sourced to the eastern Fertile Crescent, including Mesopotamia.
Around 3100 BC, a ruler identified as Narmer, or Menes, or possibly Hor-Aha unified Upper and Lower Egypt. This unification marks the transition from the Naqada III Protodynastic period into the First Dynasty of Egypt.