Reign of James II and after
After the accession of James II Balcarres was, on 3 September 1686, appointed a commissioner of the treasury, and in 1688 was made Lord Lieutenant of Fife. So much was he trusted by the king, that when the scheme for the descent of the Prince of Orange became known, the chancellor, Lord Perth, was ordered to rely on his advice and that of the Earl of Cromarty in the measures to be adopted for the defence of Scotland. Lord Melfort, secretary of state, however, who was jealous of Balcarres's influence, rejected his suggested plan of defence as too expensive, and it was determined instead to send the forces then available in Scotland southwards. Balcarres, meanwhile, was sent by the Scottish privy council to England to receive further instructions, and succeeded in reaching London.
After the king's return from Faversham, Balcarres, along with Dundee, waited on him on the morning of 17 November in his bedroom at Whitehall. At the request of the king they accompanied him on a walk in the Mall, when, having expressed his final determination to leave the country, he stated that on his arrival in France he would send Balcarres a commission to manage his civil affairs, and Dundee one to command the troops in Scotland.
After the flight of the king Balcarres waited on the Prince of Orange, to whom he was previously known through his first wife, the prince's cousin. While expressing his respect for the prince, Balcarres declined to act against the king, whereupon the prince warned him of the danger he ran if he transgressed the law. Along with Dundee, Balcarres was permitted to return to Scotland, and they arrived in Edinburgh about the end of February 1689.
The Duke of Gordon was already negotiating the surrender of the castle, when Balcarres and Dundee waited on him, and persuaded him to hold out till he saw what the Convention of Estates intended to do. On the capture of a messenger from Ireland with letters to Balcarres from the king, Balcarres was seized and confined in his own lodging. His request for permission to live in England was refused, and on account of further compromising letters sent to him by Melfort, he was confined for four months in the common jail of Edinburgh. Soon after his release he became connected with the Montgomery plot for James's restoration, and on its discovery in 1690 he left the country.