When the Arab armies of the Rashidun caliphate, commanded by Amr ibn al-As, began their invasion of Egypt in December 639, Theodore was the magister militum of the Byzantine army in the province, while Cyrus of Alexandria was both its governor (praefectus Aegypti) and the government-appointed Patriarch of Alexandria,[note 1] and Heraclius was the Roman emperor.
The Muslims besieged the fort, a massive structure 18 m (59 ft) high with walls more than 2 metres (6.6 feet) thick and studded with numerous towers and bastions and a force of some 4,000 men.
[note 2] He had brought the Ecthesis and a portion of the True Cross from Patriarch Sergius to Cyrus, and was likely on a direct commission from Emperor Heraclius.
They subsequently headed to a town in the Faiyum district named Bahnasa (not to be confused with Oxyrhynchus 50 miles further south), which was defeated and the city was captured.
According to John of Nikiû, "they compelled the city to open its gates, and they put to the sword all that surrendered, and they spared none, whether old men, babe, or woman.
When Zubayr arrived, he pointed out to ‘Amr that the Roman-garrisoned city of Heliopolis was a short distance away, and that troops from there could relieve the Siege of Babylon.
'Amr gave the following order: "Be on the watch, so that when the Roman troops come out to attack us, you may rise up in their rear, whilst we shall be on their front, and so having got them between us, we shall put them to the sword."
When Domentianus, governor of Faiyum heard of the defeat, he left his camp at Abûît and fled to Nikiû without even informing the locals that he was abandoning them to the Muslims.
[2] 'Amr then directed his troops to Delas, where he forced Apa Cyrus, pagarch of Heracleopolis Magna, to supply him and his army with boats to travel along the Nile.
John of Nikiu continues "Not content with that, 'Amr had the Roman magistrates arrested and their hands and feet fettered with chains or logs of wood: he extorted great sums of money, laid a double tax on the peasants, whom he forced to bring forage for his horses, and he committed innumerable acts of violence.
Then, with negotiations stalled, during the night of 20 December, a company of handpicked warriors, led by Zubayr, managed to scale the wall, kill the guards, and open the gates for the Muslim army to enter.
[2] The final assault of the Muslims was on Good Friday, April 6 641, and by Easter Monday the Roman troops had evacuated and began marching to Nikiû.
Many Copts who were imprisoned in Babylon, either for refusing to accept Chalcedon or on suspicion of treachery, were released from prison by the Romans, but Eudocianus, the brother of Domentianus, had them scourged and their hands cut off.
Heraclius died in February 641, two months before the fall of the Babylon Fortress, and was succeeded by his two sons Constantine III and Heraclonas as co-emperors.
Cyrus was in favour of surrendering to the Muslims, whereas Theodore wanted to continue fighting them and hoped the Emperor would send reinforcements to Egypt.
She had Heraclonas give Cyrus express permission to make peace at any price with the Arabs, but also gave him reinforcements and a new general named Constantine to replace John.
When Theodore returned to Alexandria, he dismissed Domentianus as the military commander of the garrison and exiled him from the city, replacing him with Menas, who was a non-Chalcedonian Copt and popular with the army.
Since Theodore and Cyrus' arrival in Egypt was on September 14, 641, the Feast of the Cross, a great procession was organised from their landing place to Alexandria.
Their entire path was covered in carpets, hymns were sung, and a piece of the True Cross which was earlier brought to Egypt by John, Duke of Barcaina, and stored by the monks of Tabenna, was carried with Cyrus and Theodore.
The local populace was not informed of it until an Arab army approached Alexandria to receive the tribute, and the Byzantine generals told the people not to resist.
Realising what had happened, a furious mob attempted to stone Cyrus, but he said to them "I have made this treaty in order to save you and your children" and wept before them, which calmed the riot down.
He began building his new capital, Fustat, just outside Babylon, and the Byzantine prefects and governors of Egypt either converted to Islam to retain their positions, or were replaced by Muslims.