The third century saw the growth of Christianity in Egypt and offered evidence of Coptic-speaking Christians. This growth was sporadically checked by persecution, first due to the edict of Septimius Severus in 202. Attacks on Christians by pagans in Alexandria (249) and a new edict by Decius (250) renewed the pressure. Some Christians responded with calculated avoidance of persecutors; this is the course recommended by Clement of Alexandria, and the Bishop Dionysius sought refuge in Libya during the Decian persecution. The last wave of persecution began under Diocletian in 303-4 and had a severe impact on Egypt, including the Coptic-speaking population in the Thebaid. The year of Diocletian's accession to the throne (284) became the year one in the Coptic Church calendar and all subsequent dates are labelled AM (anno martyrum). Persecution abated in 305, returned under Maximin Daia in 310-12, climaxing in the execution of the patriarch, Peter of Alexandria, on 25 November 311. The Edict of Toleration soon followed in 313.
On the one hand, the trend in the early period is toward centralization around the Bishop of Alexandria. Yet other evidence points to a diversity of Christian belief and practice in the first centuries. Gnostic thought in diverse forms was promoted in Egypt by important thinkers, above all, Valentinus (c.150). The Nag Hammadi texts, translated into Coptic in the fourth century, contain a variety of statements of anti-cosmic dualism as well as more mainstream sentiments. The writings of Epiphanius of Salamis (d. 403) circulated in Egypt and also gave lurid, perhaps exaggerated, descriptions of Gnostic worship in fourth-century Egypt, on the fringes of the Christian community. The situation is similar with the Manichaeans. Their missionaries arrived in Egypt in the third century and a variety of Manichaean literature was translated into Coptic (found at Medinet Madi and Dakleh Oasis). Manichaean doctrine, with its use of a Jesus myth and stark dualism, can be understood as another challenge to the evolving mainstream. Shenoute of Atripe (d. 465) criticized specific Gnostic and Manichaean concepts, which implies that these views were alive and threatening into the fifth century.
After the end of persecution, Christianity throughout the empire moved into a period of doctrinal clarification. The leadership assumed by the Egyptian Church through its patriarch is striking. The growth of monasticism and the conversion of Coptic-speaking areas did not reduce the influence of the patriarch, but seemed to enhance it, as holders of the office skilfully maintained the loyalty of Christians throughout Egypt. The Trinitarian controversy, prompted by the teaching of Arius, a priest of Alexandria, had an empire-wide impact. Arius taught of the Son that 'there was when He was not'. Only the Father is eternal and uncreated. In this Arius may have been, in some sense, carrying on the teaching of Origen. But he also represented conservative resistance to the authority of the patriarch. Arius was condemned by an Egyptian synod in 324, but continued controversy over his ideas led Constantine to summon an Ecumenical Council at Nicaea in 325, at which time the Nicene Creed was adopted and Arius condemned. Alexander of Alexandria and his deacon Athanasius carried the day, but negative reaction to the homoousios clause (the Son is of one essence with the Father, true God from true God) set in immediately. Athanasius became Bishop of Alexandria in 328 and from then until his death in 373 advanced Nicene theology. Exiled five times, Athanasius maintained the loyalty of clergy, monastics and Christian populace and set a pattern of centralized authority that would endure in Egypt. Nicaea was reaffirmed at the Council of Constantinople in 381, but this council also honoured Constantinople, not Alexandria, beside Rome as a leading see.
Rivalry between Constantinople and Alexandria played a role in the next theological drama: Nestorius versus Cyril of Alexandria, climaxed by the Council of Chalcedon (451). If the Nicene Creed affirmed that the Son was true God, it remained to define the relationship between divine and human in Jesus Christ. Apollinarius (d. 380) argued that the divine Word replaced the human soul in Jesus. Nestorius, Bishop of Constantinople since 428, countered by stressing the full humanity of Jesus together with his divinity and rejecting the traditional title of Theotokos for Mary. Cyril of Alexandria, bishop since 412, led the attack on Nestorius. In several works Cyril made the case for the union of God and man in Jesus Christ and crafted the statement that has symbolized Coptic Orthodoxy to the present: one incarnate nature of the Word. Cyril seems to use 'nature' (physis) as nearly equivalent to 'individual reality' (hypostasis). The Emperor Theodosius II called the third Ecumenical Council to Ephesus in 431 to resolve the issue. Alexandria and Rome were again allies. The council was a complete triumph for Cyril: his theology was affirmed and Nestorius was exiled. But as with the Nicene Creed, there was negative reaction from some and Cyril needed to negotiate a compromise Formula of Reunion with John of Antioch in 433.
Cyril died in 444 and was succeeded by Dioscorus. Various parties continued to critique the theology of Ephesus. The monk Eutyches took one extreme: the one incarnate nature was divine, since the divine nature subsumed the human. Leo of Rome countered Eutyches in a way that apparently criticized Cyril and Ephesus, though the problem was more linguistic than real. The Tome of Leo maintained Christ was one person (persona) in two natures, divine and human. Dioscorus of Alexandria convened a council at Ephesus in August 449 that supported Eutyches and deposed Flavian, Bishop of Constantinople and an ally of Rome. When imperial power changed hands, a new council (Chalcedon, 451) favored Leo's position and exiled Dioscorus. Chalcedon became the 'Robber Synod' of the Coptic Church, countering the western view of Ephesus II as the latrocinium. This was a turning point because the Egyptian Church remained loyal to Dioscorus (and his successors), in spite of the best efforts of imperial authorities.
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