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, Knox was on 8 March 1608 joined in commission with Andrew, lord Stewart, of Ochiltree, to take the matter in hand. In May he visited the king at Greenwich, and brought back instructions for a military expedition against the Isles, of which Lord Ochiltree was to be commander, assisted by a council, of which Knox was to be the head with a salary and bodyguard of his own. The expedition sailed early in August, and the castles of Dunivaig and Lochgorme in Isla having been surrendered by Angus Macdonald, Ochiltree opened a court at the castle of Aros in Mull on 15 Aug. The chieftains showing come reluctance to come to terms, Ochiltree, acting on the advice of Knox, induced them to visit him on board his vessel on pretence of a dinner and a sermon from the bishop. Having thus succeeded in kidnapping them, Ochiltree sailed to Glasgow. On his return Knox accompanied Ochiltree to London, and was commended by the king for his zeal in the service.

The chief obstacle to a settlement of the Isles was thus removed, and Knox was in February 1609 appointed one of a commission to negotiate with the chieftains for the purpose of devising a scheme for the civilisation of the Western Islands. In May he was the bearer of a confidential message from his colleagues to the king. He returned in June with instructions for a fresh expedition, of which he himself was to be the head, and he conducted the business with great credit to himself. Before the end of July he met the principal chieftains at Iona, and with their consent enacted the statutes of Icolmkill. He returned to Edinburgh in September, but immediately proceeded to London. He seems to have been detained at court till the following July, when he returned to Edinburgh, and made formal redelivery of 'the Band and Statutes of Icolmkill' before the council. On 15 Feb. 1510 he was appointed a member of the court of ecclesiastical high commission for the province of Glasgow, and on 8 May steward of the whole Western Isles, with instructions to make the castle of Dunivaig his headquarters. In the same year he was preferred to the bishopric of Raphoe (patent 28 June 1611) 'to the effect that by his panes and travellis the ignorant multitude within that Diocis may he reclamed from their superstitioun and Papishe opinionis' (, Original Letters, i. 427). He continued to hold both bishoprics till 22 Sept. 1619, when he resigned that of the Isles in favour of his eldest son, Thomas.

Having established a garrison in the castle of Dunivaig, he immediately proceeded to Ireland, and in April 1611 transmitted to Lord Salisbury a report of the state of religion in his diocese. In consequence of his report the king instructed Sir Arthur Chichester to require the Archbishop of Armagh to convene a meeting of the bishops of his province in order to consider the reformation of ecclesiastical abuses in the north of Ireland (the report of their proceedings will be found in and, Calendar of Irish State Papers, iv, 142). On 13 Oct. 1611 Chichester wrote of Knox: 'He is a good bishop for that part of the kingdom, and zealously affected to correct and reform the errors and abuses of the priests and people, and has done more good in church government in the short time of his being among them than his predecessor in all his time' (ib. iv. 149). It was probably in consequence of Chichester's report that on 13 Feb. 1612 the king authorised his admission to the privy council. As a reward for his good success in reforming the Western Isles, James addressed a letter to the council of Scotland on the 24th of the same month, requiring them (1) to make payment to him of all arrears of a pension formerly granted to him out of the duties of the Isles, in compensation for his expense in maintaining a garrison at Dunivaig; (2) to grant him a charter in feu farm for life of the Isle of Barra; (3) to restore as far as possible all the lands belonging to his bishopric that had by chance been alienated; (4) to reannex to his bishopric the abbey of Icolmkill and the priory of Ardchattan, formerly held in commendam with it. In 1614 the castle of Dunivaig was surprised by the Macdonalds, and Knox, attempting to retake it with insufficient force, was defeated and compelled to treat. He consented to solicit a lease of the crown lands of Isla for Angus Oig Macdonald, together with the proprietary rights in the castle of Dunivaig, and a free pardon for all crimes up to date, and to leave his son Thomas and his nephew John Knox of Ranfurly as hostages for his good faith. The council, however, refused these terms, and prepared to reduce the Macdonalds by force. Knox, who was alarmed for the safety of his hostages, openly counselled the employment of deceit in dealing with the Macdonalds, to be followed by their total extirpation, and the plantation of their lands by honest men from the north of Ireland and the west of Scotland. His scheme was in part realised. The Earl of Argyll desired to drive the Macdonalds into desperate courses on behalf of his kinsman, John Campbell of Calder, who had undertaken their reduction on condition of succeeding to their inheritance. One John Graham, who acted, it was supposed, at Argyll's