In the 16th year of the reign of Justinian (542/3), this prince arrived in Constantinople and began to ask the empress to allow the installation of two or three bishops for the Monophysite Arabs. The Empress graciously accepted this request. It was decided to appoint two bishops. The choice fell on the monks Jacob Bourdeana (Baradei) and Theodore, whose consecration probably took place in 543. bishops who were in the vicinity of Constantinople.

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Theodosius, Patriarch of Alexandria, gave James secret permission to ordain not only presbyters, but also bishops. And so, in the year 543, James, making a tour of his vast province, wanted to consecrate Konon and Eugene as bishops from among the persons devoted to him and to come with them to Constantinople. Theodosius, however, did not dare to ordain them, but advised him to turn to Egypt and there look for bishops for the ordination of the above-mentioned personalities. Indeed, when James arrived in Alexandria, he found them. Conon was made bishop of Tarsus, Eugene of Seleucia. Not content with these, James ordained bishops in other places as well. The most famous of them was John of Ephesus, a missionary who enjoyed the favor of Justinian; he was also the author of the first church history in Syriac. All the efforts of James would not have been complete if he had not made Seria (544) head of the Monophysites, elevating him to the rank of Patriarch of Antioch. True, in the year 547 Sergius died, and his cathedra remained unoccupied for about three years. After consulting with Theodosius of Alexandria, James appointed Paul as the second patriarch of Antioch. Thus, the activity of James was extremely important for the Monophysites. He produced something more than the Monophysites themselves could have expected.

The struggle that had taken place up to that time between the Orthodox and the Monophysites should not be presented as a struggle between the two churches; it was rather a struggle between two theological trends or two philosophical theories. Each side assumed that the incorrect teaching would destroy itself and that there would remain one true catholic church. There was no division of the churches at all. James realized that in order to strengthen the existence of Monophysitism, it was necessary to create a special Monophysite hierarchy, separate from the Orthodox. Previously, it was like this: if the Monophysites managed to get a like-minded person to the patriarchal cathedra, he remained patriarch. The government did not even think of taking any measures to eliminate it. In Alexandria it was so for a long time, until Theodosius was summoned to Constantinople, although the cathedra remained unoccupied. In the same way, in other cities, the Orthodox did not take measures to ensure that an Orthodox would exist next to the bishop of Monophysite. On the other hand, while in Antioch and other places bishops were appointed by the Diphysites, the Monophysites did not recognize them, but considered it a temporary misfortune, without losing hope of surviving it. The policy of Justin and Justinian produced such a result that the Monophysites became convinced that their dreams were unrealizable, and decided to establish their own special hierarchy. This is what James did († 578). He was the true founder of the Monophysite Church. Thus, by the beginning of the reign of Justin II, there was no longer any hope of unification. Justinian's attempt to do this was in vain.

After the death of Theodora, Justinian did not cease relations with the Monophysites and treated Anthimus favorably. In the last year of his reign, he issued an edict that the flesh of Christ was incorruptible from birth. The doctrine of the incorruptibility of the flesh of Christ, which even the moderate Monophysites (Theodosians-Sevirians) considered heresy, the emperor thus wanted to impose on the Orthodox Church as a dogma. But this could not lead to the unity of the Monophysites with the church. There is reason to suspect whether his mental faculties were not damaged by this time. What he was trying to achieve with this edict is rather difficult to decide. The Monophysites at that time were a minority of the Greek population. The edict of the emperor, even if it had been adopted, could first of all have caused confusion in Monophysitism itself; But he did not promise anything to the Orthodox Church.

The bitter fate, of course, first of all affected Archbishop Eutyches of Constantinople. He did not recognize the edict as Orthodox, since he found that, in coming out of it, he must recognize the suffering and death of Christ as illusory. On January 22, 565, Eutyches was arrested for his resistance and almost killed. Then the emperor sent him into exile. It is reported that after this a council was held in Constantinople to condemn Eutyches, in order to give this sentence ecclesiastical sanction. Information about him is found in the biographical records of his disciple Eustratius. The accusations brought against Eutyches were of the most petty and even somewhat comical nature. The most important of these was that Eutyches ate game, which was considered at that time to be a purely sybaritic delicacy (some monastic orders in the West, among other things, differed in that they permitted the eating of game on the grounds that in the rule of Benedict of Nursia it was forbidden to eat the flesh of quadrupeds only); another accusation was that Eutyches prayed to God for a long time on his knees (οτι συκοτόκυλα όρνιθίων εφαγεν, καί ότι πολλάς ώρας γονυκλισίας ποιων ηυχετο). After the council, an embassy was sent to Eutyches from his own clerics. Eutyches asked them directly: "To whom are you sent?" "To the Lord Patriarch, Bishop of Constantinople," they answered. "You are right; although I am in such a position, I still remain a patriarch, and you believe so." After this he by his own authority gave them over to excommunication.

In his place was placed John Scholasticus († August 31, 577). It is difficult to say how John Scholasticus maneuvered, refusing to sign the edict and at the same time preserving the favor of the emperor. Other bishops also refused to sign the edict of the emperor, motivating their indecision by the fact that they wanted to know the opinion of other patriarchs on this dogmatic issue. Anastasius of Antioch spoke out with all resoluteness against the edict and, expecting exile for this, wrote a farewell sermon to his flock; but Justinian died before this new measure (November 14, 565).

Justinian's successor was his nephew Justin II († October 4, 578). The new emperor did not consider it convenient either to renounce Justinian's policy or to continue it energetically. What policy he adhered to in general is shown by an anecdote: when there was a fuss in the great circus, he sent word to the blue that Justinian was dead for them, and to the green that he was alive for them. First of all, he ordered the exiled bishops to return to their places. This applied most of all to the bishops of the West. To calm the unrest of the Monophysites in Egypt, the emperor sent there Abba Photinus with some special powers.

Soon the emperor issued an edict, τό πρόγραμμα τής πίστεως, explaining his religious policy. By issuing this edict, the emperor did everything that could be done for them to please the Monophysites, without renouncing Orthodoxy. The edict repeated all the expressions experienced during the period of the Unia, which were pleasant to the Monophysites, although not entirely accurate dogmatically, and as far as possible avoided precise and decisive Orthodox terms. The emperor recognized in Christ not the other or the other, but one and the same, from both natures, divine and human, composed. Then there are expressions that are pleasant to the Monophysites: 1) One of the Holy Spirits. The Trinity suffered; 2) the only miracle and suffering; 3) Εμμανουήλ; 4) εξ έκατέρας φύσεως, έξ ών σονετέθη (strictly – the Chalcedonian preposition is not έξ, but εν); 5) μία φύσις του Θεού Λόγου σεσαρκωμένη. On the other hand, the following is noticed: 1) silence about the Council of Chalcedon (but also about others); 2) "νουύμενης" next to "ύπαρχούσης" and "έν θεωρία" when talking about διαφορά των φύσεων; 3) ή εκατέρα φύσις, preferred to the Chalcedonian δύο φύσεις, two natures, which expression occurs only once. In conclusion, the emperor asked not to argue over syllables, words, and persons, and he declared that the present form of doctrine should remain inviolable for all time. Thus, the emperor did not have any relations with the Council of Chalcedon.

This edict, union in nature, was accepted by all Orthodox, but the Monophysites did not join the Orthodox Church on the basis of it. They saw in the emperor a supporter of the "Chalcedonians", who did not live up to their expectations, which they placed on a new reign. It should be noted that Justin was married to Theodora's niece, Sophia: there was a rumor about the latter among the Monophysites that until 562 she always received communion from the Monophysite presbyter.

But the policy of peace discovered by Justin II led to a peaceful relationship between the Orthodox and the Monophysites. In the first years of Justin's reign, the following extraordinary phenomenon took place. The Theodosians strongly pressed their opponents, the Tritheites; the latter obtained permission from the emperor to arrange a dispute, the arbitrator of which was appointed John Scholasticus, Patriarch of Constantinople. The disputing parties were not allowed to refer to the writings of the Orthodox Fathers, but were allowed to cite in their favor only passages from the works of their outstanding authorities: Anthimus, Severus, Theodosius. The dispute lasted 4 days, and, in the end, the Tritheites were declared defeated.

But in the sixth year of the reign of Justin (570-571) a change occurred in the position of the Monophysites. At the insistence of John Scholasticus, the emperor decided to make a statement against the Constantinople monophysites. Their monasteries, male and female, were cordoned off by soldiers. After the forced communion from the hands of Orthodox priests and the replacement of Monophysite icons with Orthodox ones (they had previously used icons depicting Monophysite bishops and kings), it was announced that communion between these monasteries and the Orthodox Church had taken place. The stubborn monks and nuns were imprisoned. The monasteries thus converted were visited by the emperor and empress, and the obedient were rewarded with gifts. Communion was also concluded with the Monophysite hierarchs. They aroused hopes that the Council of Chalcedon would be abolished in one way or another. Apparently accepted "in their present rank," the bishops, presbyters and deacons of the Monophysites celebrated 36 liturgies together with the Orthodox. But then the Patriarch of Constantinople made an attempt to recognize their consecration as invalid and ordain them again. The narrow-minded Monophysite metropolitan of Caria, Bishop Paul of Aphrodisias, allowed the Orthodox metropolitan of Caria to consecrate him bishop of Antioch of Caria. But other Monophysite bishops, especially Stephen of Cyprus, opposed these new consecrations in the most energetic way and demanded that, if they did not recognize the validity of their consecrations, they would not recognize them (according to Nic. 19) as having a valid baptism. John abandoned this idea of reuniting them and explained that he only wanted to adorn the Monophysites with the episcopal omophorion.

The attempt to find a dogmatic middle way for reconciliation was also fruitless. The dogmatic dispute that lasted for 33 days only made it clear that the question of the dogmatic significance of the Council of Chalcedon remains essential, since the Orthodox cannot renounce this council, and the Monophysites make the abolition of this council a condition for their reunion with the Orthodox. And to the program of the union edict proposed to the Monophysites, they made several additions, which the Orthodox could not accept in their entirety, and when these additions were included in the edict only partially, the Monophysites refused to accept it.

Justin acted with great success on the Monophysites, who occupied court and state offices. He forbade them to greet him if they did not wish to be in church communion with him. Fearing for their position and property, these Monophysites heaped reproaches on their bishops and demanded that they agree to the union. In the end, a few people outwardly converted to Orthodoxy, and the stubborn ones were expelled from the capital after imprisonment. Conferences with the bishops of Monophysite were not successful even under Justin.