In the Terminal Period, we find evidence of the rule of local chiefs and the rise of the kingdoms of Upper Egypt, uniting & conquering the rest of Egypt .

The  unification of Egypt is the triumph of the mythical notion of divine kingship, a dual monarch, able to  assimilate the sacred feminine (of nature), effectively ending the Neolithic phase by making the myth of the Great Goddess part of the genesis of himself, justifying his masculine kingship, namely as the "wive of the king", the "mother of the king" or the "sister of the king"

Regarding the composition of the pantheon, nothing can be said. But the "great powers" of nature were the multiform manifestations of the sacred, associated with major "hidden" and "mysterious" processes, such as fecundity, pregnancy, birth, growth, health, regeneration, a good death and a happy afterlife. Hathor as Great Goddess of the sacred. Horus appears in the Terminal Period. It is probable that polytheism was prevailing. Each & every deity being a great manifestation of the powers of nature, a being unique in its kind with a control over a particular area of life & death. Only the flow of life itself was permanent.

Starting with simple, local  Neolithical settlements, larger agricultural areas got integrated as soon as traffic of on the Nile increased, allowing for exchanges of all kind and the realization of the fundamental unity of Egypt thanks to the Nile and its yearly gift of black Earth. The organization of larger territories and their various administrations can be observed in Amratian culture (Naqada I). The rise of societies with a central, royal authority is attested in Gerzean culture (Naqada II). Social strata reflect in funerary practices. Of course, only circumstancial evidence exists, and as such,  direct information about commoners is sparse to nonexisting.

Pharaoh united the Two Lands as a divine power, a manifestation of Horus. He was the top of the social pyramid and the only reason why the relapse into chaos did not happen.

He was not yet divine in an by himself, but and incarnation, the "best" place for the divine power to dwell in. Pharaoh was a "Follower of Horus".

The polytheism of the nomes (the area of operation of a deity, its place to be) was for the first time superceded by an active, centralizing and dominating deity : Horus.

Moreover, his name was written down. The Great Goddess had been passive, pre-historical & diffuse. Horus incarnating as Pharaoh united Egypt's divisions : the harmony of opposites.

The late Predynastic system was enhanced by the invention of writing, causing the advancement of Egyptian civilization.

A layered society emerged : a rather thin (ca.10%), but well-organized, bureaucracy around Pharaoh and his Residence, on top of a vast underlayer of illiterate farmers, laborers and common craftsmen, proficient in their work. Probably only 1% was literate.

Pharaoh was the only son of the creator Re. As the spirits of the deities abided in the sky (of the North), Pharaoh was the only god "on Earth". He was the sole mediator in who's name the temples of Egypt offered to the pantheon.

In this way, Pharaoh returned truth & justice ("Maat") to his father Re. With the exception of Re, Pharaoh was more powerful than the pantheon. At his death, Pharaoh returned to the Northern sky, to exist with the lightbeings of the circumpolar stars. There he existed with Re forever.

The gods and goddesses appear in constellations which express their various multiple interactions, actively ritualized in the temple of each nome. But national deities rise : Atum-Re (Iunu), Ptah (Mennefer) and Osiris. They are all linked with Pharaoh, the only god with direct power on Earth. The Heliopolitans dominated and proposed a creator who creates himself in the beginning (Atum) and ejects creation out of his body. In the Memphite theology, the creator created by means of divine words thought, spoken and written (manifested).

The ability to organize the resources of Egypt is formidable. Enduring common efforts to erect pyramids and other monuments stand erect today.

Deceased commoners could at best hope to "hide" as justified in the sky (of the Beautiful West). The closer they had been to Pharaoh, the more likely their happy afterlife was. Usually, their names got lost.

Numerous festivals enabled them to witness the glory of Pharaoh's rule directly. Access to and service in (parts of) the temple was also common.

The unity of Egypt was lost. Famine and civil war had occured. The country was divided.

The identity between Pharaoh & the political order was fully broken and provincialized. On the other hand, Pharaoh remained the exclusive divine mediator, son of Re.

As Lower & Upper Egypt were at war, each victor would promote "his" god to justify his kingship.

The collapse of the kingdom meant the end of a national cult (as that of Re or Ptah) and the power of Iunu and Mennefer. As a result, one returned to the deities of the nomes. The burial customs reveal the importance of interpersonal relationships in the afterlife. The priesthood attached to the temples formed a provincial élite. The provincial magnates linked their power with these cults to gain local approval.

A thriving culture existed among the poorer levels of society and a clear social development in the towns of Upper Egypt. The "collapse" of the Old Kingdom was the "end" of the old bureaucracy to the advantage of the provinces (cultural activity had been Memphis-based). The provincial milieu fostered a family-life in a loose urban structure, with the heads of the families as final authority.

The Theban nomarchs united Egypt and (when leaving Thebes) introduced Amun as their state god. Although the nomarchs assumed the Pharaonic titulary, the kingship was less centralized and a kind of feudal organization  prevailed (with taxations). Pharaoh's Osirian aspect was clearly emphasized. With it rose the importance of regeneration, magic and resurrection.

The decentralization did not last. Amun assimilated Re and the conflict between Re and Osiris was solved. As a result, a state religion saw the light again, this time with Amun-Re as "king of the gods" and "divine judge". Osiris is the "Sun of the netherworld", yet another face of Amun-Re. Yet, the scepsis and "pessimism" of the earlier period becomes a literary genre. Everybody may become an Osiris-NN.

The emerging individualism grew. The non-royal as well as  commoners had a soul, not only Pharaoh. As a result, every deceased could (assisted by the proper funerary rituals and coffin spells) be justified. This depended no longer on one's merits in the divine eyes of Pharaoh, but exclusively on the lightness of one's own mind & conscience. This feudal religious humanism fed fears expelled through magic.

Egypt's unity was lost again. Nomadic tribes infiltrated the eastern Delta ("Aziatics"). The kings of foreign lands ("Hyksos") settled in Avaris. The land was divided again in North (Lower) & South (Upper).

In the South, Amun-Re was worshipped, but the Hyksos take over Seth. The division between Horus (Re) and Seth is again apparent. They claim Egypt with vassals in Thebes. They were expelled as far as Palestine.

The Egyptians adopt foreign forms, ideas, concepts and art. The Hyksos brought the horse, the chariot and the composite bow. This paved the path for the flowering of the international humanism of the New Kingdom.

With the reunification of Egypt by the Thebans, the original power of the ideal of Pharaoh was restored and again kings were deified.

Egypt was now conceived as the center of the world and Pharaoh as the center of Egypt. The Amarna event being an extreme example of the principle. But after Amarna, Pharaoh lost his central position for good, for the gods embodied kingship.

Pharaoh was now subjected to their will too. In need, Pharaoh would appeal to Amun.

Introduction of the New Solar Theology and its focus on the course of Re hand in hand with the rest of the pantheon.

Amarna theology caused a crisis which made Amun-Re rise as the unquestioned king of the pantheon, the god of gods who existed far and near. But although his divinity was still being emphasized in the vast monumental record, Pharaoh was no longer the "god in charge" but a representative of Amun on earth. Hence, political power was slowly transferred to Amun's large priesthood who could read Amun's oracle.

The international humanism of Egypt peaked. But under Akhenaten, the Egyptians were forced to relinquish the pantheon, with as result the complete interiorization of their adherence to it. After Amarna, the central position was taken in not by the king but by the god. When evil was done, divine intervention could punish an individual. More and more the will of Amun-Re became the most important factor in religious life. The mummies of royals were no longer divine, and so could be unwrapped. All  depended on Amun's will.