Second Boer War
Boers retreat

The set-piece period of the war now largely gave way to a mobile guerrilla war, but one final operation remained. President Kruger and what remained of the Transvaal government had retreated to eastern Transvaal. Roberts, joined by troops from Natal under Buller, advanced against them, and broke their last defensive position at Bergendal on 26 August. As Roberts and Buller followed up along the railway line to Komatipoort, Kruger sought asylum in Portuguese East Africa (modern Mozambique). Some dispirited Boers did likewise, and the British gathered up much war material. However, the core of the Boer fighters under Botha easily broke back through the Drakensberg Mountains into the Transvaal highveld after riding north through the bushveld.

As Roberts's army occupied Pretoria, the Boer fighters in the Orange Free State retreated into the Brandwater Basin, a fertile area in the south-east of the Republic. This offered only temporary sanctuary, as the mountain passes leading to it could be occupied by the British, trapping the Boers. A force under General Archibald Hunter set out from Bloemfontein to achieve this in July 1900. The hard core of the Free State Boers under De Wet, accompanied by President Steyn, left the basin early. Those remaining fell into confusion and most failed to break out before Hunter trapped them. 4,500 Boers surrendered and much equipment was captured but as with Roberts's drive against Kruger at the same time, these losses were of relatively little consequence, as the hard core of the Boer armies and their most determined and active leaders remained at large.

From the Basin, Christiaan de Wet headed west. Although hounded by British columns, he succeeded in crossing the Vaal into western Transvaal, to allow Steyn to travel to meet their leaders. There was much sympathy for the Boers on mainland Europe. In October, President Kruger and members of the Transvaal government left Portuguese East Africa on the Dutch warship De Gelderland, sent by the Queen Wilhelmina of the Netherlands. Paul Kruger's wife, however, was too ill to travel and remained in South Africa where she died on 20 July 1901 without seeing her husband again. President Kruger first went to Marseille and then on to the Netherlands, where he stayed for a while before moving finally to Clarens, Switzerland, where he died in exile on 14 July 1904.
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