O'Sullivan was part of a confederation of Gaelic leaders who had gone into rebellion against Elizabeth I of England. He was aided by King Philip III of Spain, who sent an invasion force to Kinsale under the command of Don Juan del Águila. After Águila had surrendered to the queen's Lord Deputy, Lord Mountjoy, in January 1602, O'Sullivan resolved to continue the fight and rallied his forces at Dunboy.
The Crown sent a 5000 strong army under the command of Sir George Carew, Lord President of Munster, to suppress the resistance. Carew also had the support of the navy. But before the siege got under way, O'Sullivan himself and most of his forces had already marched to another of his fortresses, Ardea Castle, on the northern coast of the Beara promontory in order to secure money and supplies that had just arrived by ship from Spain.
One of O'Sullivan's cousins, who had allied himself with Carew, Owen O'Sullivan of Carrignass, then informed Carew of a weak point in the castle walls at a stairwell. Carew directed his bombardment to that point, and the walls were eventually breached. By the 10th day of the assault, the castle had been reduced to ruins, and final defeat seemed certain. MacGeoghegan sent a messenger to Carew requesting a surrender, and Carew responded by hanging the messenger in sight of the defenders. Certain of their fate, some swam to nearby Dursey Island, where they were murdered or captured in the water; the remaining defenders repelled another assault and sealed themselves in the cellar of the castle.
The assault continued relentlessly, until the castle fell on the 11th day. During the siege, crown forces raided nearby Dursey Island, where O'Sullivan families resided. Men were burned in the church, and women and children were thrown from the cliff.
On the 11th day, the castle cellar was finally overrun amid desperate hand-to-hand fighting. MacGeoghegan was hacked to pieces by Captain Power as he attempted to ignite the powder stores and blow up the cellar. All but three of those captured during the siege were hanged in the market square in nearby Castletown Berehaven. Friar Domenic Collins was interrogated by Carew, who demanded he renounce his faith for propaganda purposes prior to execution. The other two were hanged on failing to give information, and Father Collins was taken to Yougal where he was hanged, having held firm under torture.
O'Sullivan's people were besieged by enemies and the elements throughout the long journey. On their arrival at the refuge of O'Rourke's castle in Leitrim, only 35 remained, many having died in battles or from exposure and hunger. Others had settled along the route, where their descendants are known to this date as 'the Beres'.
In Leitrim, O'Sullivan sought to join with other northern chiefs to fight the English and organised a force to this end, but resistance ended when the Earl of Tyrone successfully sued for peace and swore an oath of loyalty to the crown. O'Sullivan declined this option and sought exile in Spain, where he was later murdered.