Continued desiccation forced the early ancestors of the Egyptians to settle around the Nile more permanently and forced them to adopt a more sedentary lifestyle. However, the period from 9th to the 6th millennium B.C., has left very little in the way of archaeological evidence.

The Nile valley of Egypt was basically uninhabitable until the work of clearing and irrigating the land along the banks was started. However it appears that this clearance and irrigation was largely under way by the 6th millennium. By that time, Nile society was already engaged in organized agriculture and the construction of large buildings.

At this time, Egyptians in the southwestern corner of Egypt were herding cattle and also constructing large buildings. Mortar was in use by the 4th millennium. The people of the valley and the Nile delta were self-sufficient and were raising barley and emmer, an early variety of wheat, and stored it in pits lined with reed mats. They raised cattle, goats and pigs and they wove linen and baskets. Prehistory continues through this time, variously held to begin with the Amratian culture.

Between 5500 BC and the 31st century B.C., small settlements flourished along the Nile, whose delta empties into the Mediterranean Sea. The Tasian culture was the next to appear; it existed in Upper Egypt starting about 4500 BC. This group is named for the burials found at Deir Tasa, a site on the east bank of the Nile between Asyut and Akhmim. The Tasian culture is notable for producing the earliest blacktop-ware, a type of red and brown pottery painted black on its top and interior.

The Badari culture, named for the Badari site near Deir Tasa, followed the Tasian; however, similarities cause many to avoid differentiating between them at all. The culture continued to produce the kind of pottery called blacktop-ware (although its quality was much improved over previous specimens), and was assigned the sequence dating numbers between 21 and 29. The significant difference, however, between the Tasian and Badari, which prevents scholars from completely merging the two, it's sites are Chalcolithic while the Tasian sites remained Neolithic and are thus considered technically part of the Stone Age

The Amratian culture is named after the site of el Amrah, about 120 KM (75 mi) south of Badari. El-Amreh was the first site where this culture was found unmingled with the later Gerzeh culture. However, this period is better attested at Nagada, and so is also referred to as the "Naqada I" culture. Black-topped ware continued to be produced, but white cross-line ware, a type of pottery decorated with close parallel white lines crossed by another set of close parallel white lines, began to be produced during this time. The Amratian period falls between S.D. 30 and 39. Newly excavated objects indicate that trade between Upper and Lower Egypt existed at this time. A stone vase from the north was found at El-Amreh, and copper, which is not present in Egypt, was apparently imported from the Sinai Peninsula or perhaps Nubia and an extremely small amount of gold were both definitively imported from Nubia during this time. Trade with the oases was also likely.

Naqada II

The Gerzeh culture "Naqada II", named after the site of El Gerzeh, was the next stage in cultural development, and it was during this time that the foundation for ancient Egypt was laid. The culture was largely an unbroken development out of the Amratian, starting in the Nile Delta and moving south through Upper Egypt; however, it failed to dislodge the Amratian in Nubia. The Gerzeh culture coincided with a significant drop in rainfall and farming produced the vast majority of food. With increased food supplies, the populace adopted a much more sedentary lifestyle, and the larger settlements grew to cities of about 5000 residents. It was in this time that the city dwellers started using adobe to build their cities. Copper instead of stone was increasingly used to make tools and weaponry. Silver, gold, lapis lazuli (imported from Badakhshan in what is now Afghanistan), and Egyptian faience were used ornamentally, and the cosmetic palettes used for eye paint since the Badari culture began to be adorned with reliefs.

The Old Kingdom and its royal power reached their zenith under the 4th dynasty Sneferu, the dynasty's founder, is believed to have commissioned at least three pyramids; while his son and successor Khufu (Cheops) erected the great pyramid of Giza, Sneferu had more stone and brick moved than any other pharaoh. Khufu, his son Khafra (Chephren), and his grandson Mekaure (Mycerinus) all achieved lasting fame in the construction of the Giza pyramid complex.

To organize and feed the manpower needed to create these pyramids required a centralized government with extensive powers, and Egyptologists believe the Old Kingdom at this time demonstrated this level of sophistication. Recent excavations near the pyramids led by Mark Lehner have uncovered a large city that seems to have housed, fed and supplied the pyramid workers. Although it was once believed that slaves built these monuments, a theory based on the Exodus narrative of the Hebrew Bible, study of the tombs of the workmen, who oversaw construction on the pyramids, has shown they were built by corves of peasants drawn from across Egypt. They apparently worked while the annual flood covered their fields, as well as a very large crew of specialists, including stonecutters, painters, mathematicians and priests.

The 5th dynasty began with Usekaf 2495 BC and was marked by the growing importance of the cult of the sun god Ra. Consequently, less effort was devoted to the construction of pyramid complexes than during the Fourth Dynasty and more to the construction of sun temples in Abusir. The decoration of pyramid complexes grew more elaborate during the dynasty and its last king, Unas, was the first to have the pyramid texts inscribed in his pyramid.

Egypt's expanding interests in trade goods such as ebony, incense such as myrrh and frankincense, gold, copper and other useful metals compelled the ancient Egyptians to navigate the open seas. Evidence from the pyramid of Sahure, second king of the dynasty, shows that a regular trade existed with the Syrian coast to procure cedar wood. Pharaohs also launched expeditions to the famed land of Punt, possibly the Horn of Africa, for ebony, ivory and aromatic resins.

During the 6th dynasty, the power of pharaohs gradually weakened in favor of powerful of Nomarchs. These no longer belonged to the royal family and their charge became hereditary, thus creating local dynasties largely independent from the central authority of the pharaoh. Internal disorders set in during the incredibly long reign of Pepi II Neferkare towards the end of the dynasty. His death, certainly well past that of his intended heirs, might have created succession struggles and the country slipped into civil wars mere decades after the close of Pepi II's reign. The final blow came when the 4.2 Kilo year event struck the region in the 22nd century BC, producing consistently low Nile flood levels. The result was the collapse of the Old Kingdom followed by decades of famine and strife.

First Intermediate Period

After the fall of the Old Kingdom came a roughly 200-year stretch of time known as the First Intermediate Period, which is generally thought to include a relatively obscure set of pharaohs running from the end of the sixth to the tenth and most of the 11th Dynasties. Most of these were likely local monarchs who did not hold much power outside of their nome. There are a number of texts known as "Lamentations" from the early period of the subsequent Middle Kingdom that may shed some light on what happened during this period. Some of these texts reflect on the breakdown of rule, others allude to invasion by "Asiatic bowmen". In general the stories focus on a society where the natural order of things in both society and nature was overthrown.

Senusert III was a warrior king, leading his troops deep into Nubia, and built a series of massive forts throughout the country to establish Egypt's formal boundaries with the unconquered areas of its territory. Amenemhat III is considered the last great pharaoh of the Middle Kingdom.

Egypt's population began to exceed food production levels during the reign of Amenemhat III, who then ordered the exploitation of the Faiyum and increased mining operations in the Sinai Peninsula. He also invited settlers from western Asia to Egypt to labor on Egypt's monuments. Late in his reign, the annual floods along the Nile began to fail, further straining the resources of the government. The 13th dynasty and 14th dynasty witnessed the slow decline of Egypt into the second intermediate period, in which some of the settlers invited by Amenemhat III would seize power as the Hyksos.

Second Intermediate Period and the Hyksos

The 2nd intermediate period marks a period when Egypt once again fell into disarray between the end of the Middle Kingdom and the start of the New Kingdom. This period is best known as the time the Hyksos made their appearance in Egypt, the reigns of its kings comprising the 15th dynasty.

The 13th dynasty proved unable to hold onto the long land of Egypt, and a provincial family of Levantine descent located in the marshes of the eastern Delta at Ayaris broke away from the central authority to form the 14th dynasty. The splintering of the land most likely happened shortly after the reigns of the powerful 13th dynasty Pharaohs Neferhotep I and Sobekhotep IV.

While the 14th dynasty was Levantine, the Hyksos first appeared in Egypt c. 1650 BC when they took control of Avaris and rapidly moved south to Memphis, thereby ending the 13th and 14th dynasties. The outlines of the traditional account of the "invasion" of the land by the Hyksos is preserved in the Aegyptiaca of Manetho, who records that during this time the Hyksos overran Egypt, led by Salitis, the founder of the 15th dynasty. More recently, however, the idea of a simple migration, with little or no violence involved, has gained some support. Under this theory, the Egyptian rulers of the 13th and 14th dynasties were unable to stop these new migrants from traveling to Egypt from the Levant because their kingdoms were struggling to cope with various domestic problems, including possibly famine and plague. Be it military or peaceful, the weakened state of the 13th and 14th dynasty kingdoms could explain why they rapidly fell to the emerging Hyksos power.

The Hyksos princes and chieftains ruled in the Eastern Delta with their local Egyptian vassals. The 15th dynasty rulers established their capital and seat of government at Memphis and their summer residence at Avaris.

The Hyksos Kingdom was centered in the Eastern Nile delta and central Egypt but relentlessly pushed south for the control of central and Upper Egypt. Around the time Memphis fell to the Hyksos, the native Egyptian ruling house in Thebes declared its independence and set itself up as the 16th dynasty. Another short lived dynasty might have done the same in central Egypt, profiting from the power vacuum created by the fall of the 13th dynasty and forming the Abydos dynasty.

By 1600 BC, the Hyksos had successfully moved south in central Egypt, eliminating the Abydos Dynasty and directly threatening the 16th dynasty. The latter was to prove unable to resist and Thebes fell to the Hyksos for a very short period c. 1580 BC. The Hyksos rapidly withdrew to the north and Thebes regained some independence under the 17th dynasty. From then on, Hyksos relations with the south seem to have been mainly of a commercial nature, although Theban princes appear to have recognized the Hyksos rulers and may possibly have provided them with tribute for a period.

The 17th dynasty was to prove the salvation of Egypt and would eventually lead the war of liberation that drove the Hyksos back into Asia. The two last kings of this dynasty were Seqenenre

His immediate successors continued the military campaigns, though an increasingly troubled court complicated matters. Ramesses II was succeeded by his son Merneptah and then by Merenptah's son Seti II. Seti II's throne seems to have been disputed by his half-brother Amenmesse, who may have temporarily ruled from Thebes.

Upon his death, Seti II's son Siptah, who may have been afflicted with poliomyelitis during his life, was appointed to the throne by Chanceller Bay, a West Asian commoner who served as vizier behind the scenes. At Siptah's early death, the throne was assumed by Twosret, the queen Dowager of Seti II and possibly Amenmesse's sister.

A period of anarchy at the end of Twosret's short reign saw a native reaction to foreign control leading to the execution of Bay and the enthronement of Stnakhte, establishing the 20th dynasty.

Twentieth Dynasty

The last "great" pharaoh from the New Kingdom is widely considered Ramses III, the son of Setnakhte who reigned three decades after the time of Ramses II. In 8th year of his reign, the sea people invaded Egypt by land and sea. Ramesses III defeated them in two great land and sea battles. He claimed that he incorporated them as subject people and settled them in Southern Canaan, although there is evidence that they forced their way into Canaan. Their presence in Canaan may have contributed to the formation of new states in this region such as Philistia after the collapse of the Egyptian Empire. He was also compelled to fight invading Libyan tribesmen in two major campaigns in Egypt's Western Delta in his 6th year and 11th year respectively.

The heavy cost of these battles slowly exhausted Egypt's treasury and contributed to the gradual decline of the Egyptian Empire in Asia. The severity of these difficulties is stressed by the fact that the first known strike action in recorded history occurred during Year 29 of Ramesses III's reign, when the food rations for the Egypt's favored and elite royal tomb-builders and artisans in the village of Dier El Madina could not be provisioned. Something in the air prevented much sunlight from reaching the ground and also arrested global tree growth for almost two full decades until 1140 BC. One proposed cause is the Hekla 3 Eruption in Iceland, but the dating of that event remains in dispute.

Following Ramesses III's death there was endless bickering between his heirs. Three of his sons would go on to assume power as Ramses IV, and Ramses VIII, respectively. However, at this time Egypt was also increasingly beset by a series of droughts, below-normal flooding levels of the Nile, famine, civil unrest and official corruption. The power of the last pharaoh, Ramses XI, grew so weak that in the south the Theban high priests of Amun became the effective de facto rulers of Upper Egypt, while Smendes controlled Lower Egypt even before Ramesses XI's death. Smendes would eventually found the 21st dynasty at Tanis.

Third Intermediate Period

After the death of Ramses XI, his successor Smendes ruled from the city of Tanis in the north, while the high priests at Thebes had effective rule of the south of the country, whilst still nominally recognizing Smendes as king. In fact, this division was less significant than it seems, since both priests and pharaohs came from the same family. Piankh, assumed control of Upper Egypt ruling from Thebes, with the northern limit of his control ending at Al-Hibah. (The High Priest Herihor had died before Ramesses XI, but also was an all-but-independent ruler in the latter days of the king's reign.) The country was once again split into two parts with the priests in Thebes and the pharaohs at Tanis. Their reign seems without other distinction, and they were replaced without any apparent struggle by the Libyan kings of the 22nd dynasty.

The Persian king Cambyses assumed the formal title of Pharaoh, called himself Mesuti-Re ("Re has given birth"), and sacrificed to the Egyptian gods. He founded the 27th dynasty. Egypt was then joined with Cyprus and Phoenicia in the sixth satrapy of the Achaemenid Empire.

Cambyses' successors Darius I the great and Xerxes pursued a similar policy, visited the country, and warded off an Athenian attack. It is likely that Artaxerxes I and Darius II visited the country as well, although it is not attested, and did not prevent the Egyptians from feeling unhappy.

During the war of succession after the reign of Darius II, which broke out in 404 BC, they revolted under Amyrtaeus and regained their independence. This sole ruler of the 28th dynasty died in 399, and power went to the 29th dynasty. The 30th dynasty was established in 380 BC and lasted until 343 BC. Nectanebo II was the last native king to rule Egypt.

Artaxerxes III reconquered the Nile valley for a brief period (343–332 BC). In 332 B.C. Mazaces handed over the country to Alexander the great without a fight. The Achaemenid Empire had ended, and for a while Egypt was a satrapy in Alexander's empire. Later the Ptolemais and then the Romans successively ruled the Nile valley.

Ptolemaic dynasty

In 332 BC Alexander III of Macedon conquered Egypt with little resistance from the Persians. He was welcomed by the Egyptians as a deliverer. He visited Memphis, and went on a pilgrimage to the oracle of Amun at the Oasis of Siwa. The oracle declared him the son of Amun. He conciliated the Egyptians by the respect he showed for their religion, but he appointed Greeks to virtually all the senior posts in the country, and founded a New Greek city, Alexandria, to be the new capital. The wealth of Egypt could now be harnessed for Alexander's conquest of the rest of the Persian Empire. Early in 331 BC he led his forces away to Phoenicia, never returning to Egypt.

Following Alexander's death in Babylon in 323 BC, a succession crisis erupted among his generals. Perdiccas ruled the empire as regent for Alexander's half-brother Arrhidaeus, who became Philip III of Macedon, and Alexander's infant son Alexander IV of Macedon. Perdiccas appointed Ptolemy, one of Alexander's closest companions, to rule Egypt in the name of the joint kings. However, as Alexander's empire disintegrated, Ptolemy soon established himself as ruler in his own right. Ptolemy successfully defended Egypt against an invasion by Perdiccas in 321 BC and consolidated his position in Egypt and the surrounding areas during the wars of the Diadochi (322–301 BC). In 305 BC, Ptolemy took the title of Pharaoh. As Ptolemy I Soter ("Saviour"), he founded the Ptolemaic dynasty that was to rule Egypt for nearly 300 years.

The later Ptolemais took on Egyptian traditions by marrying their siblings, had themselves portrayed on public monuments in Egyptian style and dress, and participated in Egyptian religious life. Hellenistic culture thrived in Egypt well after the Muslim conquest. The Egyptians soon accepted the Ptolemais as the successors to the pharaohs of independent Egypt. Ptolemy's family ruled Egypt until the Roman conquest of 30 BC.

All the male rulers of the dynasty took the name Ptolemy. Ptolemaic queens regnant, some of whom were the sisters of their husbands, were usually called Cleopatra, Arsinoe or Berenice. The most famous member of the line was the last queen, Cleopatra, known for her role in the Roman political battles between Julius Caesar and Pompey, and later between Octavian and Mark Antony. Her apparent suicide at the conquest by Rome marked the end of Ptolemaic rule in Egypt.