In June 1632, Morton became
Bishop of Durham, which he held by canonical right until his death in 1659, although parliament claimed to deprive him of it in 1647. Complaints were later made against him to the
House of Commons by his prebendary,
Peter Smart. He showed forbearance in claiming the rights of the palatinate, was liberal in almsgiving, and maintained poor scholars at the universities. On his journey to Scotland in 1633,
Charles I and his suite were received by Morton in princely style; six years later, in May 1639, he again entertained Charles at the beginning of the
First Bishops' War. The next year, in the month of August, the Scots crossed the
River Tweed, and pushed on to the city of
Durham. The cathedral clergy fled, and Morton himself retired into
Yorkshire. Early in 1641 he was in London attending Parliament, and was nominated a member of the sub-committee to prepare matters for the consideration of the abortive committee of the lords appointed on 1 March—the day of
William Laud's committal to the
Tower of London—to take cognisance of innovations in religion. In the following December a mob threatened to drag him out of his coach when on his way to the
House of Lords. Morton never took his seat in the lords again. Two days later, 29 December, he joined in
John Williams' protest against the legality of all acts done in the enforced absence of the
Lords Spiritual. For this he and his 11 associates were next day impeached of
high treason on
William Prynne's motion; and the same night they were all committed to the Tower, with the exception of Morton and the aged
Robert Wright,
Bishop of Lichfield, who were allowed to remain in the house of the
usher of the black rod. After four months' imprisonment Morton was released without a trial, and remained unmolested at
Durham House, in
The Strand, till April 1645, when he was again brought before the bar of the House of Commons on the charges of baptising the infant daughter of the Earl of Rutland according to the rites of the Church of England, and of refusing to surrender the seal of the
County palatine of Durham. He was committed to the custody of the
serjeant-at-arms for six months. On the abolition of
episcopacy in 1646 an annual income was assigned to him, but without indications of by whom it was to be paid not being specified. He obtained a sum of £1,000 from the committee at
Goldsmiths' Hall, which he employed in paying his debts and purchasing an annuity. In 1648 he was driven from Durham House soldiers, who took forcible possession of it. He then resided with his friends, the Earl and Countess of Rutland, at
Exeter House in The Strand; and the passed his time with royalist lay friends. Returning to London on horseback, he fell in with Christopher, son and heir of
Henry Yelverton. Christopher did not recognise the bishop. To his inquiry who he was, Morton replied, 'I am that old man, the Bishop of Durham, in spite of all your votes;' asked where he was going, his answer was, 'To London, to live there a little while, and then to die.' Ultimately, Yelverton invited him to his house at
Easton Maudit, ten miles from
Northampton. Morton became a member of the family, and tutor to Henry, his eldest son. At Easton Maudit, Morton held secret
ordinations. Yelverton died in 1654. Morton died there on 22 September 1659. He was buried in the Yelverton chapel of the parish church. His chaplain,
John Barwick, preached the funeral sermon. He died unmarried. ==Patronage==