Little is known for certain of Cyril's early life. He was born c. 376, in the small town of Didouseya, Egypt, modern-day El-Mahalla El-Kubra. A few years after his birth, his maternal uncle Theophilus rose to the powerful position of Patriarch of Alexandria. His mother remained close to her brother and under his guidance, Cyril was well educated. His writings show his knowledge of Christian writers of his day, including Eusebius, Origen, Didymus the Blind, and writers of the Church of Alexandria. He received the formal Christian education standard for his day: he studied grammar from age twelve to fourteen (390–392), rhetoric and humanities from fifteen to twenty (393–397) and finally theology and biblical studies (398–402).
In 403 he accompanied his uncle to attend the "Synod of the Oak" in Constantinople, that deposed John Chrysostom as Archbishop of Constantinople. The prior year, Theophilus had been summoned by the emperor to Constantinople to apologize before a synod, over which Chrysostom would preside, on account of several charges which were brought against him by certain Egyptian monks. Theophilus, had them persecuted as Origenists. Placing himself at the head of soldiers and armed servants Theophilus had marched against the monks, burned their dwellings, and ill-treated those whom he captured. Theophilus arrived at Constantinople with twenty-nine of his suffragan bishops, and conferring with those opposed to the Archbishop, drafted a long list of largely unfounded accusations against Chrysostom,  who refused to recognize the legality of a synod in which his open enemies were judges. Chrysostom was subsequently deposed.
Patriarch of Alexandria
Theophilus died on 15 October 412, and Cyril was made Pope or Patriarch of Alexandria on 18 October 412, but only after a riot between his supporters and those of his rival Archdeacon Timotheus. According to Socrates Scholasticus, the Alexandrians were always rioting.
Thus, Cyril followed his uncle in a position that had become powerful and influential, rivalling that of the prefect in a time of turmoil and frequently violent conflict between the cosmopolitan city's Pagan, Jewish, and Christian inhabitants. He began to exert his authority by causing the churches of the Novatianists to be closed and their sacred vessels to be seized.
Dispute with the Prefect
Orestes, Praefectus augustalis of the Diocese of Egypt, steadfastly resisted Cyril's ecclesiastical encroachment onto secular prerogatives.
Tension between the parties increased when in 415, Orestes published an edict that outlined new regulations regarding mime shows and dancing exhibitions in the city, which attracted large crowds and were commonly prone to civil disorder of varying degrees. Crowds gathered to read the edict shortly after it was posted in the city's theater. Cyril sent the grammaticus Hierax to discover the content of the edict. The edict angered Christians as well as Jews. At one such gathering, Hierax, read the edict and applauded the new regulations, prompting a disturbance. Many people felt that Hierax was attempting to incite the crowd into sedition. Orestes had Hierax tortured in public in a theatre. This order had two aims: the first was to quell the riot, the other to mark Orestes' authority over Cyril.
Socrates Scholasticus recounts that upon hearing of Hierex's severe and public punishment, Cyril threatened to retaliate against the Jews of Alexandria with "the utmost severities" if the harassment of Christians did not cease immediately. In response to Cyril's threat, the Jews of Alexandria grew even more furious, eventually resorting to violence against the Christians. They plotted to flush the Christians out at night by running through the streets claiming that the Church of Alexander was on fire. When Christians responded to what they were led to believe was the burning down of their church, "the Jews immediately fell upon and slew them" by using rings to recognize one another in the dark and killing everyone else in sight. When the morning came, the Jews of Alexandria could not hide their guilt, and Cyril, along with many of his followers, took to the city’s synagogues in search of the perpetrators of the massacre.
According to Socrates Scholasticus, after Cyril rounded up all the Jews in Alexandria, he ordered them to be stripped of all possessions, banished them from Alexandria, and allowed their goods to be pillaged by the remaining citizens of Alexandria. Scholasticus indicates that all the Jews were banished, while John of Nikiû says only those involved in the ambush. Susan Wessel says that while it is not clear whether Scholasticus was a Novationist, (whose churches Cyril had closed), he was apparently sympathetic towards them, and makes clear Cyril's habit of abusing his episcopal power by infringing on the rights and duties of the secular authorities. Wessel says "...Socrates probably does not provide accurate and unambiguous information about Cyril's relationship to imperial authority.
Nonetheless, with Cyril's banishment of the Jews, however many, "Orestes [...] was filled with great indignation at these transactions, and was excessively grieved that a city of such magnitude should have been suddenly bereft of so large a portion of its population." Because of this, the feud between Cyril and Orestes intensified, and both men wrote to the emperor regarding the situation. Eventually, Cyril attempted to reach out to Orestes through several peace overtures, including attempted mediation and, when that failed, showed him the Gospels, which he interpreted to indicate that the religious authority of Cyril would require Orestes' acquiescence in the bishop's policy. Nevertheless, Orestes remained unmoved by such gestures.
This refusal almost cost Orestes his life. Nitrian monks came from the desert and instigated a riot against Orestes among the population of Alexandria. These monks' had resorted to violence 15 years before, during a controversy between Theophilus (Cyril's uncle) and the "Tall Brothers"; The monks assaulted Orestes and accused him of being a pagan. Orestes rejected the accusations, showing that he had been baptised by the Archbishop of Constantinople. A monk named Ammonius, threw a stone hitting Orestes in the head. The prefect had Ammonius tortured to death, whereupon the Patriarch honored him as a martyr. However, according to Scholasticus, the Christian community displayed a general lack of enthusiasm for Ammonius's case for martyrdom. The prefect then wrote to the emperor Theodosius II, as did Cyril.
Murder of Hypatia
Prefect Orestes enjoyed the political backing of Hypatia, an astronomer, philosopher and mathematician who had considerable moral authority in the city of Alexandria, and who had extensive influence. At the time of her death, she was likely over sixty years of age. Indeed, many students from wealthy and influential families came to Alexandria purposely to study privately with Hypatia, and many of these later attained high posts in government and the Church. Several Christians thought that Hypatia's influence had caused Orestes to reject all reconciliatory offerings by Cyril. Modern historians think that Orestes had cultivated his relationship with Hypatia to strengthen a bond with the Pagan community of Alexandria, as he had done with the Jewish one, in order to better manage the tumultuous political life of the Egyptian capital. A mob, led by a lector named Peter, took Hypatia from her chariot and murdered her, hacking her body apart and burning the pieces outside the city walls.
Neoplatonist historian Damascius (c. 458 – c. 538) was "anxious to exploit the scandal of Hypatia's death", and attributed responsibility for her murder to Bishop Cyril and his Christian followers. Damascius's account of the Christian murder of Hypatia is the sole historical source attributing direct responsibility to Bishop Cyril. Some modern studies represent Hypatia's death as the result of a struggle between two Christian factions, the moderate Orestes, supported by Hypatia, and the more rigid Cyril. According to lexicographer William Smith, "She was accused of too much familiarity with Orestes, prefect of Alexandria, and the charge spread among the clergy, who took up the notion that she interrupted the friendship of Orestes with their archbishop, Cyril." Scholasticus writes that Hypatia ultimately fell "victim to the political jealousy which at the time prevailed". News of Hypatia's murder provoked great public denouncement, not only against Cyril but against the whole Alexandrian Christian community.
Conflict with Nestorius
Another major conflict was between the Alexandrian and Antiochian schools of ecclesiastical reflection, piety, and discourse. This long running conflict widened with the third canon of the First Council of Constantinople which granted the see of Constantinople primacy over the older sees of Alexandria and Antioch. Thus, the struggle between the sees of Alexandria and Antioch now included Constantinople. The conflict came to a head in 428 after Nestorius, who originated in Antioch, was made Archbishop of Constantinople.
Cyril gained an opportunity to restore Alexandria's pre-eminence over both Antioch and Constantinople when an Antiochine priest who was in Constantinople at Nestorius' behest began to preach against calling Mary the "Mother of God" (Theotokos). As the term "Mother of God" had long been attached to Mary, the laity in Constantinople complained against the priest. Rather than repudiating the priest, Nestorius intervened on his behalf. Nestorius argued that Mary was neither a "Mother of Man" nor "Mother of God" as these referred to Christ's two natures; rather, Mary was the "Mother of Christ" (Greek: Christotokos). Christ, according to Nestorius, was the conjunction of the Godhead with his "temple" (which Nestorius was fond of calling his human nature). The controversy seemed to be centered on the issue of the suffering of Christ. Cyril maintained that the Son of God or the divine Word, truly suffered "in the flesh." However, Nestorius claimed that the Son of God was altogether incapable of suffering, even within his union with the flesh. Eusebius of Dorylaeum went so far as to accuse Nestorius of adoptionism. By this time, news of the controversy in the capital had reached Alexandria. At Easter 429 A.D., Cyril wrote a letter to the Egyptian monks warning them of Nestorius' views. A copy of this letter reached Constantinople where Nestorius preached a sermon against it. This began a series of letters between Cyril and Nestorius which gradually became more strident in tone. Finally, Emperor Theodosius II convoked the Council of Ephesus (in 431) to solve the dispute. Cyril selected Ephesus as the venue since it supported the veneration of Mary. The council was convoked before Nestorius's supporters from Antioch and Syria had arrived and thus Nestorius refused to attend when summoned. Predictably, the Council ordered the deposition and exile of Nestorius for heresy.
However, when John of Antioch and the other pro-Nestorius bishops finally reached Ephesus, they assembled their own Council, condemned Cyril for heresy, deposed him from his see, and labelled him as a "monster, born and educated for the destruction of the church". Theodosius, by now old enough to hold power by himself, annulled the verdict of the Council and arrested Cyril, but Cyril eventually escaped. Having fled to Egypt, Cyril bribed Theodosius' courtiers, and sent a mob led by Dalmatius, a hermit, to besiege Theodosius' palace, and shout abuse; the Emperor eventually gave in, sending Nestorius into minor exile (Upper Egypt).
Cyril died about 444, but the controversies were to continue for decades, from the "Robber Synod" of Ephesus (449) to the Council of Chalcedon (451) and beyond.