Finding him firmly established in Tyrconnel, the government acquiesced in his usurpation, and on 12 March 1558 Mary addressed letters to him, promising, on his good behaviour, to reward him ‘of our lyberalytie accordyng to your gooddeserts.’ Meanwhile Shane, foiled in his intention of conquering Tyrconnel, was wreaking his vengeance on his unhappy wife, Margaret O'Donnell, Calvagh's sister, and, in order apparently to punish him for his cruelty, Calvagh towards the end of 1560 enlisted a number of redshanks. His purpose was applauded by government, to whom Shane was becoming a formidable enemy, and an offer was made to him in April 1561 to create him Earl of Tyrconnel. Affairs were in this position when, on 14 May, Calvagh and his wife were captured by O'Neill at the monastery of Kill-donnell, close to Fort Stewart, near the upper end of Lough Swilly. It has been suggested that Calvagh was betrayed by his wife out of a supposed passion for Shane O'Neill (Bagwell, ii. 21); but the ‘Four Masters’ simply say that ‘some of the Kinel-Connell informed O'Neill that Calvagh was thus situated without guard or protection,’ and their statement is corroborated by the account in the ‘Book of Howth’ (Cal. Carew MSS. iv. 204). Calvagh and his wife were carried off by O'Neill into Tyrone, the former to be kept in close and secret confinement, the latter to become the mistress of her captor. When Sussex invaded Tyrone in June, Calvagh was hurried about from ‘one island and islet to another, in the wilds and recesses of Tyrone,’ to avoid a rescue. Force and diplomacy proved equally unavailing to induce O'Neill to surrender him.
Meanwhile Calvagh was suffering the most excruciating tortures. He had to wear an iron collar round his neck fastened by a short chain to gyves on his ankles, so that he could neither stand up nor lie down. Finally, about the beginning of 1564, O'Neill released him on condition that he surrendered Lifford, together with his claims to the overlordship of Inishowen and paid a considerable ransom. His wife was to remain in durance till ransomed by her relations, the MacDonnells. It is doubtful whether Calvagh had any intention of being bound by the conditions thus extorted from him. His followers refused to surrender Lifford, and Shane, who had managed to lay hold of his son Con and threatened to put him to death for his father's breach of faith, was obliged to starve them into submission.
On regaining his liberty, Calvagh proceeded to Dublin to solicit aid from the government, but met with a cold reception. He was reminded that no O'Donnell ever came to Dublin to do the state service, and so being denied the aid he sought, ‘he burst out into such a weeping as when he should speak he could not, but was fain by his interpreter to pray license to weep, and so went his way without saying anything.’ Shortly afterwards, though forbidden to leave the kingdom, he slipped over to England, and laid his grievances before Elizabeth in person. He reached London in a state of great destitution, no man, as he said, being willing to trust him one meal's meat. Hearing the story of his sufferings from his own lips, Elizabeth acknowledged that she was not ‘without compassion for him in this calamity, specially considering his first entry thereto was by taking part against Shane when he made war against our good subjects there,’ and ordered the lord-justice, Sir Nicholas Arnold, to make some provision for him. But Calvagh had no confidence in Arnold's impartiality, and preferred to remain in England. The attempt to govern Ireland by conciliating O'Neill ended in failure, and, with the appointment of Sir Henry Sidney in the summer of 1565, Calvagh's hopes of restoration grew brighter. He returned to Ireland with Sidney at the beginning of the following year. To the demand for his restoration, O'Neill roundly declared that he should never come into his country if he could keep him out. On 15 June 1566 Sidney issued orders to restore Calvagh, and there was even some talk of creating him Earl of Tyrconnel.
In September Sidney, accompanied by Calvagh, Kildare, and Maguire, marched northwards through Tyrone into Tyrconnel. Donegal, Ballyshannon, Beleek, Bundrowes, and Sligo, the last with a proviso in favour of O'Conor Sligo, were formally handed over to Calvagh. On 20 Oct., at Ballyshannon, he made public confession of his obligations to the queen, acknowledged her sovereignty, promised to assist at hostings, to attend parliament, to hold his lands from the crown, and ‘if the queen should hereafter be pleased to change the usages or institutions of this country, and to reduce it to civil order and obedience to her laws like the English parts of this realm,’ to render her his assistance and support. ‘By this journey,’ wrote Sidney, ‘your majesty hath recovered to your obedience a country of seventy miles in length and forty-eight miles in breadth, and the service of 1,000 men now restored to O'Donnell, and so united and confirmed in love towards him as they be ready to follow him whithersoever he shall lead them.’ Calvagh, however, did not
