[6] Morton was ordained in 1592, and held the office of university lecturer in logic till in 1598 when he obtained the living of All Saints' Church, Long Marston, in Yorkshire.

He conducted disputations with Roman Catholics; Herbert Croft, who became Bishop of Hereford, was claimed as Morton's convert to the Church of England.

When in London he lodged at the deanery of St Paul's Cathedral with John Overall, in whose house he enjoyed the society of Isaac Casaubon, who became a friend; and met Abraham Scultetus, Giovanni Diodati, and Pierre Du Moulin.

[6] Two significant works came out of this period, in which Morton had to deal with local issues outside the grander scope of the allegiance oath controversy to which he had devoted his efforts.

His tenure as bishop coincided with a watershed moment in opinion, namely a changed view of the relative threat of Catholicism and Protestant nonconformity.

In 1621, he served on the commission for granting a dispensation to George Abbot, Archbishop of Canterbury, for the casual homicide of a keeper in Bramshill Park.

[6] 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.

He showed forbearance in claiming the rights of the palatinate, was liberal in almsgiving, and maintained poor scholars at the universities.

[6] 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.

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.

[6] 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.

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.'

[6] His attitude towards the Roman Catholic Church was hostile; he was one of the only three bishops who, according to a statement made to Gregorio Panzani, the papal envoy, by Richard Montagu, were 'counted violently bent against the Papists'.

[11] Lubbertus was a leading contra-Remonstrant and Morton was one of his significant English supporters in the conflict over the appointment of Conrad Vorstius at the University of Leiden.

[12] One of Morton's last acts before his death was to publish a denial that he had in a speech in the House of Lords acknowledged the fiction of the Nag's Head Consecration of Matthew Parker, Archbishop of Canterbury.

He also bequeathed a silver-gilt chalice and paten of large size for the use of the chapel recently added to the manor-house by Henry Yelverton.

[6] In the 1680s Richard Baxter, who as a schoolboy received confirmation from Morton in Durham, called him "one of the learnedest and best bishops that ever I knew".

[13] He gained a reputation as a Protestant controversialist, and published numerous works against Roman Catholicism, prominent among them being the Apologia catholica (1605) and A Catholicke Appeale (1609).