As Joint Secretary of State in Scotland 1691–1695, he played a key role in suppressing the Jacobite rising of 1689 and was forced to resign in 1695 for his part in the Massacre of Glencoe.

During the 1639-1651 Wars of the Three Kingdoms, Scottish Royalists and Covenanters both agreed monarchy itself was divinely ordered but disagreed on the nature and extent of Royal authority versus that of the church.

In 1681, the future James VII & II was sent to Edinburgh as Lord High Commissioner and in August, the Scottish Parliament passed the Succession Act.

[5] The Scottish Test Act passed at the same time required all public officials and MPs to swear 'to uphold the true Protestant religion' but also to acknowledge the supremacy of Royal authority in all religious matters.

Stair's last political action was in the debate over Article XXII of the Act of Union, concerning Scottish representation in the unified Parliament; it was approved on 7 January 1707 and he died in his lodgings the following day, his death being attributed to apoplexy.