Lagganmore was part of the Wars of the Three Kingdoms - the linked civil wars in Scotland, England and Ireland between 1639 and 1651 that ended with the execution of Charles I and the rise of Oliver Cromwell. But the Scottish theatre of the war was always tangled up with the older feuds between the Highland clans, and Lagganmore was as much a chapter in the centuries-long quarrel between Clan Donald and Clan Campbell as it was a battle of the Royalist and Covenanter sides. Alasdair Mac Colla was a MacDonald, fighting for a Royalist cause that conveniently overlapped with his own clan's project of recovering ancestral lands in Kintyre that the pro-government Campbells had taken. The politics of 17th-century Scotland made strange neighbours of cause and grudge.

Alasdair Mac Colla came to Scotland in June 1644 at the head of a group of Irish professional soldiers, sent by Confederate Ireland and the Earl of Antrim ostensibly to support the Royalists. He joined forces with the Marquess of Montrose and helped fight the brilliantly successful Royalist campaign of 1644-45, winning battle after battle until Montrose's army was destroyed at Philiphaugh in September 1645. Mac Colla then left Montrose, took some of his Irish troops and a contingent of MacDonalds, and returned to Kintyre to renew the war against the Campbells. Early 1646 was spent on a fruitless siege of Craignish Castle, during which Archibald Campbell, the Tutor of Craignish, repeatedly taunted Mac Colla by challenging him to single combat. By spring the Campbells had raised a counter-force under John Campbell of Lochnell and Donald Campbell of Bragleen.

Most of what is known about the actual fighting comes from local folklore. Contemporary written sources are nearly silent. Bragleen and Lochnell's force, mainly Clan Campbell with men of several associated clans, assembled in Glen Euchar to attack Mac Colla. Zachary MacCallum of Poltalloch joined them - by one tradition because he happened to be in the area, though as a political ally of the Campbell chief Argyll he was probably with the force from the start. Mac Colla had perhaps 1,500 men: his veteran Irish troops along with MacDougall and MacAulay levies. The Campbell force was perhaps 700. Mac Colla's advance guard attacked first and routed them. Lochnell escaped, Bragleen was captured (and reportedly escaped later), and Poltalloch was said to have come close to killing Mac Colla himself before being struck down by an opponent with a scythe.

What happened after the battle is what made Lagganmore notorious. According to long-standing local tradition, Mac Colla's Royalist soldiers drove a number of prisoners from the battle, along with Campbell women and children from the surrounding district, into a barn and set it on fire. Almost everyone inside burned to death. Only two women - or, by another version, one woman and Campbell of Bragleen - were said to have escaped. The place became known as Sabhal nan Cnamh, the Barn of Bones, and the name has stayed in the folklore of Argyll for nearly four centuries. The massacre was part of a series of revenge-driven atrocities committed by both sides during the Wars of the Three Kingdoms; the Campbells had burned MacDonald homes in their turn, and the cycle of violence in 1640s Scotland did not stop with combatants.

The dead at Sabhal nan Cnamh were not soldiers. They were prisoners who had surrendered and were entitled to quarter, women and children from villages near the battlefield, civilians caught in the long quarrel between two clans they could not have stopped. Their names are not recorded; the folklore preserved the place and the act but not the people who died. They were not statistics either - they were families, neighbours, the workers of small farms in Glen Euchar in the spring of 1646. Mac Colla went on to lose decisively at Knocknanuss in Ireland in 1647 and was killed in the aftermath. The Wars of the Three Kingdoms eventually ended. The Barn of Bones, and the names that were never written down, remain part of the geography of Argyll.