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 Complaints were frequently made of Brent's long sojourns in London, where he had a house of his own in Little Britain. On 23 Aug. 1629 he was knighted at Woodstock by the king, who was preparing to pay a state visit to Oxford. On 24 Aug. Brent entertained the French and Dutch ambassadors at Merton, and on 27 Aug. gave a dinner to the king and queen. In 1629–30 he was admitted to the freedom of the city of Canterbury honoris causa (Hist. MSS. Comm. 9th Rep. 1635). In August 1636 Brent presented Prince Charles and Prince Rupert for degrees, when Laud, who had become chancellor in 1630, was entertaining the royal family. In 1638 Laud held a visitation of Merton College, and insisted on many radical reforms. Laud stayed at the college for many weeks, and found Brent an obstinate opponent. Laud complains in his 'Diary' that 'the warden appeared very foul.' Some outrageous charges of maladministration were indeed brought against Brent by some of those whom Laud examined, but the visitor took no public proceedings against Brent on these grounds. His letters to the warden are, however, couched in very haughty and decisive language. Brent ultimately gained the victory over Laud. The tenth charge in the indictment drawn up against the archbishop in 1641 treats of the unlawful authority exercised by him at Merton in 1638. The warden came forward as a hostile witness at Laud's trial. His testimony as to Laud's intimacy with papists and the like was very damaging to the archbishop, but it does not add much to his own reputation. Laud replied to Brent's accusations in his 'History of the Troubles and Trial' (Anglo-Cath. Libr. iv. 194). On the outbreak of the civil wars Brent sided with the parliament. Before Charles I entered Oxford (29 Oct. 1642), the warden had abandoned Oxford for London. On 27 Jan. 1644–1645 Charles I wrote to the loyal fellows at Merton that Brent was deposed from his office on the grounds of his having absented himself for three years from the college, of having adhered to the rebels, and of having accepted the office of judge-marshal in their ranks. He had also signed the covenant. The petition for the formal removal of Brent, to which the king's letter was an answer, was drawn up by John Greaves, Savilian professor of geometry. On 9 April the great William Harvey was elected to fill Brent's place: but as soon as Oxford fell into the hands of Fairfax, the parliamentary general (24 June 1646), Brent returned to Merton, and apparently resumed his post there without any opposition being offered him. In 1647 Brent was appointed president of the famous parliamentary commission, or visitation, ordered by the parliament 'for the correction of offences, abuses, and disorders' in the university. The proceedings began on 3 June, but it was not until 30 Sept. that the colleges were directed to forward to Merton their statutes, registers, and accounts to enable Brent and his colleague to really set to work. On 12 April 1648 Brent presented four of the visitors for the degree of M.A. Early in May of the same year Brent showed more mercy than his colleagues approved by 'conniving' at Anthony à Wood's retention of his postmastership in spite of his avowed royalism. Wood tells us that he owed this favour to the intercession of his mother, whom Brent had known from a girl. On 17 May 1649 Fairfax and Cromwell paid the university a threatening visit, and malcontents were thenceforth proceeded against by the commission with the utmost rigour. But Brent grew dissatisfied with its proceedings. The visitors claimed to rule Merton College as they pleased, and, without consulting the warden, they admitted fellows, masters, and bachelors of arts. On 13 Feb. 1650–1 he sent a petition of protest against the conduct of the visitors to parliament. The commissioners were ordered to answer Brent's complaint, but there is no evidence that they did so, and in October 1651 Brent retired from the commission. On 27 Nov. following he resigned his office of warden, nominally in obedience to an order forbidding pluralities, but his refusal to sign 'the engagement,' which would have bound him to support a commonwealth without a king or a house of lords, was probably the more direct cause of his resignation. Brent afterwards withdrew to his house in Little Britain, London, and died there on 6 Nov. 1652. He was buried in the church of St, Bartholomew the Less on 17 Nov. Wood states that he had seen an epitaph in print on Brent by one 'John Sictar, a Bohemian exile, whom Brent had provisioned' in his lifetime.

Brent's daughter Margaret married Edward Corbet of Merton College, a presbyterian, on whom Laud repeatedly refused to confer the living of Chartham. Brent's literary work was small. In 1620 he translated into English the 'History of the Council of Trent' by Pietro Soane Polano (i.e. Pietro Sarpi). A second edition appeared in 1629, and another in 1676, Archbishop Abbot had caused the Latin original to be published for the first time in 1619 in London. In 1625, 'at the importunity of George [Abbot], archbishop of Canterbury,' Brent edited and republished the elaborate defence of the church