[2] At the opening of parliament on the visit of Charles to Scotland in 1633, Rothes bore the sceptre, but then he resolutely opposed the king's ecclesiastical policy.

In case of the rejection of the king's demands, Hamilton had threatened that Charles would march north to Scotland, and Rothes joined his kinsman Alexander Leslie in preparing for armed resistance.

On 22 March Rothes and other nobles, with one thousand musketeers, went to the palace of Lord-treasurer Traquair at Dalkeith, seized much ammunition and arms, and brought the royal ensigns of the kingdom (the crown, sword and sceptre) to Edinburgh Castle.

Rothes accompanied the army of General David Leslie in June to Dunse Lew, and was one of the commissioners appointed to treat with the king.

The Scots anticipated Charles's war plans by invading England, and on 27 August 1640 Rothes, in command of a regiment, and as one of the committee of the estates, accompanied Leslie's army across the River Tweed; according to Gilbert Burnet, the Scots were encouraged by a message sent by Viscount Savile, for three people: Rothes, the Earl of Argyll, and Johnston of Warriston.

After the occupation of Newcastle, Rothes was one of the commissioners sent to London in November to conclude the negotiations after the Treaty of Ripon, and after the pacification was arranged he remained in England at the court of Charles.