The Argylls became operational shortly after the Jacobite victory at Killiecrankie in July 1689 and were based at Perth to counter an advance towards Edinburgh. This threat never arose and in July 1690 they moved to Fort William as part of the force commanded by Colonel John Hill, the military governor tasked with pacifying the Highlands. This included Colonel Hill's own regiment which was commanded by Lt-Colonel James Hamilton and is often confused with the Argylls. The next 18 months were spent retaking or destroying strongpoints captured by anti-government forces after Killiecrankie, including Castle Stalker, Duart Castle and Cairnburgh Castle.