After the queen's escape from Lochleven, he assembled his dependents against her at Langside on 13 May 1568; and on the 19 May he was, with the Earl of Glencairn, appointed Lieutenant of the Western parts, with special instructions to watch the castle of Dumbarton, and prevent the entrance into it of provisions or reinforcements or fugitives. For his special services he obtained a gift of the abbey of Paisley. While returning one evening in May 1570 from the army that had demolished the castle of the Hamiltons, he was seized by some of the Hamiltons' dependents, and carried a prisoner to Draffen, whence he was shortly afterwards removed to Argyle. Calderwood states that he remained in Argyle for twelve months, but he was probably set at liberty in February 1570 [1571 New Style]; for when the house of Paisley surrendered to the regent at that time, the lives of those within it were granted on this condition. Notwithstanding the utmost efforts of Glencairn and Sempill, the castle of Dumbarton continued to hold out, until, on 1 April 1571, its rock was scaled by his cousin Thomas Crawford of Jordanhill.