After the Stuart restoration of 1660, the Scottish government brought bishops back into the Church of Scotland. Ministers who refused to renounce the 1638 National Covenant - about 270 of them, a third of the kirk's clergy - lost their pulpits. Most were from the southwest, the heartland of the Covenanting tradition. They kept preaching in fields, at gatherings called Conventicles, sometimes drawing thousands of listeners despite official threats of fines and imprisonment. In 1665, the Second Anglo-Dutch War wrecked the Scottish economy. By 1666, in the southwest, the government's troops under General James Turner were collecting fines from people who could not pay. The rising began on 13 November at St John's Town of Dalry, traditionally said to have started when local Covenanters intervened to stop soldiers tormenting an elderly man. Whatever the spark, within days an irregular army was on the move.

James Wallace of Auchens, a soldier who had served in the civil wars in Ulster and Scotland, took command on 21 November with Joseph Learmont as his deputy. The goal was Glasgow, but a government army under Tam Dalyell of the Binns blocked the road. So Wallace turned east toward Edinburgh, hoping to deliver a petition to the Privy Council and gather reinforcements. By Lanark on 26 November the rebels numbered about 1,100. They paused there to publicly subscribe to the Covenant. The next day they reached Colinton, just outside the city, but Edinburgh's gates stayed shut. Two weeks of winter marching had drained them. With Dalyell's army to the west, Wallace moved east and then south, along the line of the Pentland Hills, halting near Rullion Green to wait for the stragglers. There, in the late afternoon, Dalyell's deputy William Drummond appeared with a troop of cavalry.

Wallace drove off Drummond's first probe, but the main government force was only four miles away. Too close to escape. He formed his men on the high ground above the Glencorse River and waited. Dalyell deployed below. Three times the government soldiers attacked the Covenanter left, and three times they were thrown back. On the fourth attempt, in the fading light, a small body of Covenanter cavalry moved across the field to relieve their pressed left flank - and exposed the right. Drummond saw it and struck. Outnumbered along the whole line, the Covenanter position collapsed. Around 50 men died, many of them killed in the pursuit through the dusk. Among the dead were John Cruickshank and Andrew McCormack, two Presbyterian ministers who had crossed from Ulster to join the rising. Estimates of prisoners ranged from 80 to 140. Wallace himself escaped, eventually reaching the Netherlands, where he died in 1678.

On 19 December 1666, nine prisoners were beheaded at the cross in Glasgow. Their names are recorded on a memorial: Robert Bunton, John Hart, Robert Scot, Matthew Patoun, John Richmond, James Johnston, Archibald Stewart, James Winning, John Main. They died because they would not acknowledge the authority the government claimed over their consciences. Hugh Mackail, a young preacher recently returned from the Netherlands, was tortured for information before his execution on 22 December. John Neilson of Corsock was tortured and hanged on 14 December. In all, 36 prisoners were executed in Edinburgh, Glasgow, and Ayr. The rest, the survivors of the field and the dungeon both, were put on ships and sent to Barbados as bonded labour. Most never came home. The Pentland Rising had lasted barely three weeks from the spark at Dalry to the rout at Rullion Green, and the government response made it clear: religious dissent would be answered with the whip, the rope, and the transport hulk.

After Rullion Green the Lauderdale administration tried, briefly, a more moderate policy. It did not last. Persecution returned and deepened, and by the 1680s the Borders and southwest were caught in what Covenanting memory calls the Killing Time - the years from 1679 to 1688 when soldiers shot dissenters at the roadside, when ministers were hunted across the moors, when refusing to swear the oath could cost you your life. The 19th century rediscovered the Covenanters as martyrs and raised cairns and memorials to them across Scotland. The Covenanter's Grave still stands on the drove road across the Pentlands, a stone cairn at OS reference NT078521. Below it, the ground where 1,100 weary men made their last stand on a November afternoon is now a quiet stretch of upland pasture, unchanged in any way that matters since the night their position collapsed and they ran into the dark.