It was during this process that Brian pursued an alternative means of consolidating his control, not merely over the Province of Ulster, but over Ireland as a whole. In contrast to its structure elsewhere, the Roman Catholic Church in Ireland was centred, not around the bishops of dioceses and archbishops of archdioceses, but rather around monasteries headed by powerful abbots who were members of the royal dynasties of the lands in which their monasteries resided. Among the most important monasteries was Armagh, located in the Province of Ulster. Brian's advisor, Maelsuthain O'Carroll, documented in the 'Book of Armagh' that, in the year 1005, Brian donated twenty-two ounces of gold to the monastery and declared that Armagh was the religious capital of Ireland to which all other monasteries should send the funds they collected. This was a clever move, for the supremacy of the monastery of Armagh would last only so long as Brian remained the High King. Therefore, it was in the interest of Armagh to support Brian with all their wealth and power. It is interesting that Brian is not referred to in the passage from the 'Book of Armagh' as the 'Ard Rí' —that is, High-King— but rather he is declared "Imperator Scottorum," or "Emperor of the Irish" ("Scottorum" then being the common Late Latin term for the Irish: Ireland was usually referred to in Latin as "Scotia Major" while Scotland was referred to as "Scotia Minor").

Though it is only speculation, it has been suggested that Brian and the Church in Ireland were together seeking to establish a new form of kingship in Ireland, one that was modelled after the kingships of England and France, in which there were no lesser ranks of regional Kings – simply one King who had (or sought to have) power over all in a unitary state. In any case, whether as High King or Emperor, by 1011 all of the regional rulers in Ireland acknowledged Brian's authority. No sooner had this been achieved than it was lost again.

Máel Mórda mac Murchada of Leinster had only accepted Brian's authority grudgingly and in 1012 rose in rebellion. The Cogadh Gaedhil re Gallaibh relates a story in which one of Brian's sons insults Máel Morda, which leads him to declare his independence from Brian's authority. Whatever the actual reason was, Máel Morda sought allies with which to defy the High-King. He found one in a regional ruler in Ulster who had only recently submitted to Brian. Together they attacked the Province of Meath, where the former High King Máel Sechnaill sought Brian's help to defend his Kingdom. In 1013 Brian led a force from his own Province of Munster and from southern Connacht into Leinster; a detachment under his son, Murchad, ravaged the southern half of the Province of Leinster for three months. The forces under Murchad and Brian were reunited on 9 September outside the walls of Dublin. The city was blockaded, but it was the High King's army that ran out of supplies first, so that Brian was forced to abandon the siege and return to Munster around the time of Christmas.

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The Battle of Clontarf

Máel Morda was aware that the High King would return to Dublin in 1014 to try once more to defeat him. He may have hoped that by defying Brian, he could enlist the aid of all the other regional rulers Brian had forced to submit to him. If so, he had been sorely disappointed; while the entire Province of Ulster and most of the Province of Connacht failed to provide the High King with troops, they did not, with the exception of a single ruler in Ulster, provide support for Máel Morda either. His inability to obtain troops from any rulers in Ireland, may explain why Máel Morda sought to obtain troops from rulers outside of Ireland. He instructed his subordinate and cousin, Sigtrygg, the ruler of Dublin, to travel overseas to enlist aid.

Sigtrygg sailed to Orkney, and on his return stopped at the Isle of Man. These islands had been seized by the Vikings long before and the Hiberno-Norse had close ties with Orkney and the Isle of Man. There was even a precedent for employing Norsemen from the isles; they had been used by Sigtrygg's father, Amlaíb Cuarán, in 980, and by Sigtrygg himself in 990. Their incentive was loot, not land. Contrary to the assertions made in theCogadh Gaedhil re Gallaibh, this was not an attempt by the Vikings to reconquer Ireland. All of the Norsemen, both the Norse-Gaels of Dublin and the Norsemen from the Isles, were in the service of Máel Morda. It should be remembered that the High King had 'Vikings' in his army as well; mainly the Hiberno-Norse of Limerick (and probably those of Waterford, Wexford, and Cork as well), but, according to some sources, a rival gang of Norse mercenaries from the Isle of Man. Essentially this could be characterised as an Irish civil war in which foreigners participated as minor players.

Along with whatever troops he obtained from abroad, the forces that Brian mustered included the troops of his home Province of Munster, those of Southern Connacht, and the men of the Province of Meath, the latter commanded by his old rival Máel Sechnaill mac Domnaill. He may have outnumbered Máel Morda's army, since Brian felt secure enough to dispatch a mounted detachment under the command of his youngest son, Donnchad, to raid southern Leinster, presumably hoping to force Máel Morda to release his contingents from there to return to defend their homes. Unfortunately for the High King, if he had had a superiority in numbers it was soon lost. A disagreement with the King of Meath resulted in Máel Sechnaill withdrawing his support (Brian sent a messenger to find Donnchad and ask him to return with his detachment, but the call for help came too late). To compound his problems, the Norse contingents, led by Sigurd Hlodvirsson, Earl of Orkney and Brodir of the Isle of Man, arrived on Palm Sunday, 18 April. The battle would occur five days later, on Good Friday.

The fighting took place just north of the city of Dublin, at Clontarf (now a prosperous suburb). It may well be that the two sides were evenly matched, as all of the accounts state that the Battle of Clontarf lasted all day. Although this may be an exaggeration, it does suggest that it was a long, drawn-out fight.

There are many legends concerning how Brian was killed, from dying in a heroic man-to-man combat to being killed by the fleeing Viking mercenary Brodir while praying in his tent at Clontarf. After his death, his body was taken to Swords Co. Dublin to be waked and then on to Armagh to be buried. His tomb is said to be in the north wall of St. Patrick's Cathedral in the city of Armagh.