Justinian, the successor of Justin in 527, settled the quarrel between the two Alexandrian bishops by summoning them both to Constantinople, and then sending them into banishment.  But this had no effect in healing the divisions in the Egyptian church; and for the next half-century the two parties ranged themselves, in their theological or rather political quarrel, under the names of their former bishops, and called themselves Gaianites and Theodosians.  Nor did the measures of Justinian tend to lessen the breach between Egypt and Constantinople.  He appointed Paul to the bishopric, and required the Egyptians to receive the decrees of the council of Chalcedon.

After two years Paul was displaced either by the emperor or by his flock; and Zoilus was then seated on the episcopal throne by the help of the imperial forces.  He maintained his dangerous post for about six years, when the Alexandrians rose in open rebellion, overpowered the troops, and forced him to seek safety in flight; and the Jacobite party then turned out all the bishops who held the Greek faith.

When Justinian heard that the Jacobites were masters of Egypt he appointed Apollinarius to the joint office of prefect and patriarch of Alexandria, and sent him with a large force to take possession of his bishopric.  Apollinarius marched into Alexandria in full military dress at the head of his troops; but when he entered the church he laid aside his arms, and putting on the patriarchal robes began to celebrate the rites of his religion.  The Alexandrians were by no means overawed by the force with which he had entered the city; they pelted him with a shower of stones from every corner of the church, and he was forced to withdraw from the building in order to save his life.  But three days afterwards the bells were rung through the city, and the people were summoned to meet in the church on the following Sunday, to hear the emperor’s letter read.  When Sunday came the whole city flocked to hear and to disobey Justinian’s orders.  Apollinarius began his address by threatening his hearers that, if they continued obstinate in their opinions, their children should be made orphans and their widows given up to the soldiery; and he was as before stopped with a shower of stones.  But this time he was prepared for the attack; this Christian bishop had placed his troops in ambush round the church, and on a signal given they rushed out on his unarmed flock, and by his orders the crowds within and without the church were put to rout by the sword, the soldiers waded up to their knees in blood, and the city and whole country yielded its obedience for the time to bishops who held the Greek faith.