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 spiritual lords. 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