Although Boaventura sued for peace in early May, the Portuguese rebuffed the offer. The main rebel group of about 12,000 men, women and children under Boaventura retreated into the Cablac mountains and prepared to make a final stand around the Riac and Leolaco peaks. Isolated and surrounded in a 35 km2 area, they constructed an earthwork  reinforced by wood and stone. Many also went into hiding in underground caves.On 11 June the Portuguese siege began. When the Manufahistas attempted a breakthrough, over 3,000 died in the fighting. Boaventura himself escaped, but in late July he surrendered. The siege ended on 21 July. The Times of London in August called the siege of Cablac a "major battle" in which over 3,000 Timorese were killed or wounded and another 4,000 captured. According to Pearse, a passenger on the Eastern and Australian ship, who left an account of his observations and discussions in Dili, he was told that the rebel leaders were to be exiled to Africa and other prisoners to Atauro Island.

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