Covenanting wars
Immediately on the subscription of the Covenant in Edinburgh, the powerfully organized body, known as the Tables, made arrangements for enforcing its acceptance throughout the whole country and gathering funds to support military detachments.
Sir Thomas Burnett of Lees was one of their commissioners for the district north of the Grampians. He and other Commissioners paid a preliminary visit to Aberdeen in early July 1638 where they were told politely but firmly by the town's magistrates and other leading citizens that they had no legal authority to exact the subscriptions demanded. The deputation returned in force on the 20th of that month headed by the Earl of Montrose, then an earnest Covenanter, with several notable Covenanting preachers with them. The latter were promptly refused the pulpits of the city churches. The university promptly denounced the Covenant as unlawful, and three of the leading preachers, Henderson, Dickson, and Cant, made a temporary retreat to the safety of Sir Thomas's Muchalls Castle.
In March 1639, some 11000 men under Montrose and Huntly were told to 'reduce' the northern districts to subjection, but on 12 March 1639, Montrose and Argyll wrote to Sir Thomas Burnett of Leys to reassure him. Aberdeen made strong representations to Montrose who retired to Strathbogie whilst his army were admitted into the town for accommodation, most of the opposition to them having fled. Sir Thomas Burnett was one of the tribunal established to sit on 2 April in Greyfriars Church there and on following days, to force 'malignants' to subscribe to the Covenant under pain of confiscation of their goods. Viscount Aboyne's part of the Covenanting army then encamped at Muchalls and ransacked Burnett's property, despite his protestations.
Further Covenanters arrived at Aberdeen in 1644 under the Earl of Argyll and the Earl Marischal, and during that occupation a Committee of the Estates for Northern Business met there, to which a petition was presented by Lord Fraser, Sir Thomas Burnett of Leys, Patrick Leslie the Provost, and others, complaining of their losses by the quartering of troops and seeking redress from the first and readiest effects of the 'malignants' which come to hand.
Later that year, Montrose, raised to a Marquess and now opposed to the Covenant, marched north to suppress opposition to the King's cause. Leys clearly thought the Covenanters had gone too far in open rebellion against their King, and summoned Montrose to his castle at Crathes to sup with him, whereupon he offered Montrose arms, horses, and 5000 merks. Montrose accepted the arms and horses but refused the money. Sir Thomas and his son were subsequently the only known Covenanters who were protected by the Marquess. In the meantime Sir Thomas armed and organised half of his retainers to protect his lands from robber bands now all too plentiful due to the state of the north. At the same time Sir Thomas petitioned the Scottish Parliament for an exemption from excise and other heavy taxation being raised for Covenanting armies being sent to England, and for aid against marauding Highlanders.
It would appear that Sir Thomas was refused exemption for he subsequently sent his whole silver plate to Edinburgh to be melted down, by way of a loan, and also loaned money to the Marquess of Argyll.
