Traveling up the Nile to Berber, Baker spent a year wandering along the Atbara River and the Blue Nile, hunting and learning Arabic before returning to Khartoum, from which he and his wife launched an expedition up the White Nile in December 1862. Arriving at Gondokoro, the Bakers met the British explorers John Hanning Speke and James Augustus Grant, who had reached Lake Victoria and the Nile from the East African coast. In 1863-1864 Baker and his wife discovered and explored the eastern shore of Lake Albert, visited Kamrasi, the ruler of Bunyoro, and after many delays returned to London, where Baker wrote an extremely popular book about his explorations and the horrors of the Sudanese slave trade.
In the spring of 1869 Baker was approached by Ismail, the khedive of Egypt, to lead an Egyptian expedition to the Upper Nile to extend Egyptian control to Lake Victoria, to claim the territory for Egypt, and to end the slave trade. Baker was consequently appointed governor general of Equatoria Province and sailed up the Nile with a large expedition of 1200 troops, the most expensive expedition to penetrate Africa.