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 farmed an estate in co. Fermanagh; the loss of a leg led him to sell his land and become a linen-yarn merchant. He was a man of high character, but, relying on a fraudulent security, he was reduced to poverty, and 100l. a year was allowed him by his creditors. Of four brothers William was the only one who reached maturity. His early education was at Enniskillen, under Dr. Tew, and in the endowed school under Dr. Noble. His mother's half-brother, Daniel Viridet, D.D., an accomplished scholar, prepared him for Trinity College, Dublin, which he entered as a pensioner on 30 June 1781, his tutor being Richard Stack, D.D. A close friendship subsisted between him and [q. v.], son of the presbyterian minister of Enniskillen, and afterwards lord chancellor of Ireland. Magee became scholar of Trinity in 1784, graduated B.A. in October 1785 (gold medallist), and was elected fellow in June 1788. The election excited great interest; for Magee was not merely a hard student, but his lively wit made him extremely popular. His own inclination was towards the church, but his uncle Viridet designed him for the bar. An arrangement was actually entered into with [q. v.], by which Tone's brother was to represent Magee at the qualifying dinners in the Middle Temple, London. But Provost [q. v.], who had quarrelled with Stack, refused to his pupil the usual dispensation from orders, and Magee was ordained deacon at St. Kevin's Church, Dublin, on 25 May 1790, by [q. v.], bishop of Dromore. His first sermon is said to have been preached at St. Peter's, Drogheda; his first in Dublin was in Trinity College Chapel, on 30 Jan. 1791, and made a great impression by its eloquent discussion of the revolutionary tendencies of the day in politics and religion. Magee modestly refused the request of the senior board for its publication.

As junior dean Magee exerted himself, with some success, to improve the discipline of Trinity College. He was less successful in challenging the right of the provost to reassign the pupils of the outgoing fellows, and incurred the rebuke of the visitors. On his marriage in 1793 he retained his fellowship, the prohibition in the college statutes being practically in abeyance. In 1795 he was appointed Donnellan lecturer. Taking the subject of prophecy, he delivered twenty-two discourses, and made some progress in preparing them for the press, but they were never published. A tendency of blood to the head led him to leave Dublin in 1797. Settling on a farm at Rathfarnham, five miles off, he had his father for a neighbour. Relaxing none of his academic duties, he contrived to find more time for study.

On successive Good Fridays in 1798 and 1799 he delivered in Trinity College Chapel two sermons on the doctrine of the atonement, forming the basis of a work of which the first edition appeared in 1801. This was a brilliant polemic, lively, erudite and miscellaneous, against the positions of the Priestley school of unitarians; in successive editions its proportions were expanded, and it included much criticism of Belsham's ‘improved version’ (1808) of the New Testament. The popularity of the work was great, and it was not unacceptable to the older school of ‘rational dissenters,’ among whom Magee had many family connections. His wife's uncle,, M.D. [q. v.], an old-fashioned Arian, and the first president of the Manchester Academy (now Manchester New College, Oxford), helped him to a criticism of Priestley. Of unitarian replies to Magee's work the most considerable was by [q. v.]

Magee became senior fellow on 3 March 1800, and was appointed professor of mathematics. He visited Oxford and Cambridge with his friend Plunket in 1803, and was welcomed as a pillar of orthodoxy. Spencer Perceval is said to have designed him in 1811 for the vacant see of Oxford, but the appointment of a Dublin man was unprecedented. When his friend Plunket was a candidate for the representation of Dublin University in parliament in 1812, Magee supported him, although he could not follow Plunket in desiring catholic emancipation, nor was support of Plunket the way to preferment. He resigned his fellowship in 1812, on accepting (23 Sept.) two college livings, the rectories of Cappagh, co. Tyrone, and Killeleagh, co. Down, vacated by the death of Stack. A unique tribute to his popularity as fellow was the presentation to him of a silver vase and tray by members of the Historical Society and scholars of Trinity. He resided at Cappagh, and threw himself into parochial work, especially in connection with the parochial schools. In 1813 he was appointed dean of Cork, and resigned Killeleagh. He was chaplain to the lord-lieutenant, and became famous as a preacher, his sermons lasting an hour. In Cork his health suffered from the climate; his educational policy was obnoxious to the Roman catholics; and he incurred odium by insisting on a standing order, in consequence of which the performance of a Roman catholic burial service in his churchyard was interrupted.

In 1819 Magee was made bishop of Raphoe,