The main work of the council was to confirm the condemnation issued by edict in 551 by the Emperor Justinian against the Three Chapters. These were the Christological writings and ultimately the person of Theodore of Mopsuestia (d. 428), certain writings against Cyril of Alexandria's Twelve Anathemas accepted at the Council of Ephesus, written by Theodoret of Cyrrhus (d. c. 466), and a letter written against Cyrillianism and the Ephesian Council by Ibas of Edessa (d. 457).
The purpose of the condemnation was to make plain that the Great Church, which followed a Chalcedonian creed, was firmly opposed to Nestorianism as supported by the Antiochene school which had either assisted Nestorius, the eponymous heresiarch, or had inspired the teaching for which he was anathematized and exiled. The council also condemned the teaching that the Virgin Mary could not be rightly called the Mother of God (Gk. Theotokos) but only the mother of the man (Gk. anthropotokos) or the mother of Christ (Gk. Christotokos).
Justinian hoped that this would contribute to a reunion between the Chalcedonians and monophysites in the eastern provinces of the Empire. Various attempts at reconciliation between these parties within the Byzantine Empire were made by many emperors over the four centuries following the Council of Ephesus, none of them successful. Some attempts at reconciliation, such as this one, the condemnation of the Three Chapters and the unprecedented posthumous anathematization of Theodore – who had once been widely esteemed as a pillar of orthodoxy—causing further schisms and heresies to arise in the process, such as the aforementioned schism of the Three Chapters and the emergent semi-monophysite compromises of monoenergism and monotheletism. These propositions assert, respectively, that Christ possessed no human energy but only a divine function or principle of operation (purposefully formulated in an equivocal and vague manner, and promulgated between 610 and 622 by the Emperor Heraclius under the advice of Patriarch Sergius I of Constantinople) and that Christ possessed no human will but only a divine will, "will" being understood to mean the desires and appetites in accord with the nature (promulgated in 638 by the same and opposed most notably by Maximus the Confessor).
The Council was presided over by Eutychius, Patriarch of Constantinople, assisted by the other three eastern patriarchs or their representatives. Pope Vigilius was also invited; but even though he was at this period resident in Constantinople (to avoid the perils of life in Italy, convulsed by the war against the Ostrogoths), he declined to attend, and even issued a document forbidding the council from preceding without him (his 'First Constitutum'). For more details see Pope Vigilius.
The council, however, proceeded without the pope to condemn the Three Chapters. And during the seventh session of the council, the bishops had Vigilius stricken from the diptychs for his refusal to appear at the council and approve its proceedings, effectively excommunicating him personally but not the rest of the Western Church. Vigilius was then imprisoned in Constantinople by the emperor and his advisors were exiled. After six months, in December 553, he agreed, however, to condemn the Three Chapters, claiming that his hesitation was due to being misled by his advisors. His approval of the council was expressed in two documents, (a letter to Eutychius of Constantinople on 8 December 553, and a second "Constitutum" of 23 February 554, probably addressed to the Western episcopate), condemning the Three Chapters, on his own authority and without mention of the council.