James, earl of Morton; but after the fall of Morton Douglas was denounced a traitor, and in April 1581 the priory was restored to Seton.
Although he became nominally a protestant, Seton appears to have remained on good terms with his catholic instructors; and on an English jesuit apprehended on 1 March 1583 a letter was found from him to the master of the seminary at Rome (Calderwood, History of the Kirk of Scotland, iii. 702). Thereupon the general assembly of the kirk sent a deputation to the king and council to cause him to undergo trial for the offence (ib. p. 706). The king promised that he should be sent for and confronted with the jesuit (ib. p. 707). The result is not stated, but it seems to have been satisfactory to the king, if not to the kirk, for the same year the prior accompanied his father, Lord Seton, on an embassy to France.
After the fall of Arran, in 1585, Seton was chosen one of the king's new privy councillors, under the act passed on 10 Dec. On 27 Jan. 1586 he was chosen an extraordinary lord of session, when he took his seat as prior of Pluscardine; and on 16 Feb. he was appointed an ordinary lord, as Baron Urquhart, the lands of Urquhart and Pluscardine having been united into a barony and granted to him. As the genuineness of his protestantism was suspected, the kirk succeeded in insisting that before he undertook office as ordinary lord he should partake of the communion at the time appointed by the ministers of Edinburgh (‘Book of Sederunt,’ quoted in Brunton and Haig, Senators of the College of Justice, p. 199). On 4 April 1588 he was named a commissioner for assessing the taxation of 10,000l. to defray expenses in connection with the king's approaching marriage (Reg. P. C. Scotl. iv. 269). On 28 May 1593 he was appointed lord president of the court of session, and from this time may be ranked as one of the principal political advisers of the king. On 9 Jan. 1596 he was named one of the eight auditors of the exchequer known as the Octavians (Reg. P. C. Scotl. v. 255), of whom he was regarded as the chief. Shortly afterwards he gave indications of his catholic sympathies by a speech at the meeting of the convention of estates, in which he urged the recall of the banished catholic earls, on the ground that it was safer they should return than remain abroad to plot against the state (Calderwood, v. 438). It was scarce to be expected that the kirk authorities would coincide with this view of the matter, and its commissioners ordained that, on 2 Nov., he should appear before the synod of Lothian for dealing in favour of the Earl of Huntly (ib. p. 448). Of this, says Calderwood, he ‘purged himself very largely’ (ib.) But the kirk remained unsatisfied in regard to this and other matters; and the feeling against him found special expression in the tumult in Edinburgh in the following December, one of the requests made by the four commissioners of the kirk sent to the king immediately afterwards being that he should ‘remove from his company’ Lord-president Seton and others ‘thought to be authors of the chief troubles of the kirk,’ and known to be representatives of the ‘excommunicated earls’ (Calderwood, v. 513–514; ‘Narrative of the King’ in Reg. P. C. Scotl. v. 362–3). Not long afterwards the king accepted the resignation of the Octavians. Nevertheless the kirk, by its violence, obtained no substantial benefit, but the opposite; and the triumph of the king over the unruly city was completed by the appointment of Lord Urquhart as its lord provost, an office which he held for nine years in succession.
On 4 March 1597–8 Seton obtained a letter under the great seal erecting the barony of Fyvie into a free lordship, with the title of a lord of parliament; and shortly afterwards he was intrusted with the guardianship of the king's second son, Prince Charles, afterwards Charles I. In December he was also chosen one of the king's new privy councillors, on the limitation of the number to thirty-one (Reg. P. C. Scotl. v. 500). But though closely identified with the general policy of the king, he on two remarkable occasions displayed an independence which says much for his integrity and honour. When the king by a personal appeal—which virtually amounted to a demand—attempted to reverse a decision of the court of session passed in favour of Robert Bruce, whom the king had deprived of his stipend, Seton rose and told him that this was a question of law, in which they were sworn to do justice according to their consciences and the statutes of the realm; that of course the king could command them to the contrary, but that in that case he and every honest man on the bench would either vote according to his conscience, or resign and not vote at all (Nicolson to Cecil, 16 March 1598–9, quoted in Tytler, History of Scotland, ed. 1864, iv. 270). Still more creditable to his honour and manliness—for here he was not placed in any official dilemma—was his opposition at the convention at Perth, in June 1600, to the king's foolish demand for money to maintain a
