Clones was a border area even in medieval times, and no doubt suffered burning and devastation when armies were marching through it journeying elsewhere

It has already been mentioned that Muircertach Ua Lochlainn passed this way on his journey to Connacht in 1161; in 1432 the Galls and Mac Mahon returned to Airghialla and Dartraighe Coininse was burned; in 1457 Maguire burned Dartry Coininse and the town of Eoghan Mac Mahon namely Lis na ngabur,i.e. Lisnagore near Newbliss. The Mac Mahons controlled the Clones area and they began to control the church as well. An increasing number of them intruded themselves into positions such as vicar, rector, abbot, coarb. Other families looked towards Clones also. The Mac Domhnaill,Mac Donnells, family ruled part of Clankelly. Due to the emergence of the Maguire family as rulers of Fermanagh, and the Mac Mahons as rulers of Monaghan, it was inevitable that Mac Domhnaill would be crushed. From 1441 onwards the Mac Domhnaill family and the Maguires were in conflict until finally Mac Domhnaill was driven from Clankelly, and in 1520 the family was no longer referred to as Mac Domhnaill of Clankelly but as Mac Domhnaill of Con -innsi, Mac Donnell of Conons.

In 1591 the ballybetagh of Ballecovenche was held by the Mac Donnells as freeholders under. Mac Mahon. This area became part of county Monaghan and gives the county its peculiar appearance at this particular point. In 1486 there was a conflict between Art Mac Donnell of Clankelly and James Mac Mahon.Donnchadh. Mac Mahon, the parson of Clones, and Gilla Patrick 0 Connolly) the abbot of Clones) were helping James In the ensuing struggle Art was slain.

There was also a struggle between the Mac Mahons and the Maguires for the Corbania,i.e. church lands, of Clones. By 1535 it appears that Maguire succeeded in dislodging Mac Mahon and in asserting the rule of Maguire over the area.

The Mac Domhnaill family had probably some claim to Clones, or at least they may have felt they had. No doubt some of the chieftains were buried there, such as Mac Donnell of Clankelly, Cormac son of Art, a charitable and a truly hospitable man died and was interred in clones. This was in 1499. Perhaps the incident of 1486 was an effort that Mac Donnell was making to try and to gain dome compensation in Clones for what he was losing to Maguire in Clankelly.

In the Round Tower cemetery there is a tombstone that deserves a special mention. It is a stone version of the ridge roofed reliquary coffin in which the dead person's bones were placed. It is a solid block of hard sandstone that was designed to stand above the grave but with features of its wooden prototype. There are outlines of imitation locks and hasps of a wooden reliquary coffin. It has also been influenced by the style of church building at the time of its construction which was in the eight or ninth century. It has a steep roof and the eastern end has a carved mitred head,and the western end has carved animal heads. The tomb, which is due east and west, is five feet ten inches long, and three feet high. Most often the founder of monasteries was buried in the most important one, or possibly the one in which he died. As Clones was such this is likely St.Tiarnach's grave. It was regarded in the nature of a shrine and there was always a special significance attaching to it. The tomb was known by the people as the priest's tomb. There was a rivalry between the Mac Mahons and the Mac Domhnaill families as to which of them the tomb rightfully belonged. An I8th., century inscription cut on it has been defaced, by one of the rival claimants no doubt, that it is now illegible.