In 1897 Macdonald was in London when he was appointed leader of another expedition to Uganda, ostensibly to review the northern boundaries. Although Uganda had been declared a British Protectorate the British were concerned that France or Italy would claim some of the unoccupied territory. General
Herbert Kitchener was advancing up the Nile towards
Khartoum, which he would capture at the
Battle of Omdurman on 2 September 1898. However, a French column under
Jean-Baptiste Marchand was striking across Africa from
Senegal to
Fashoda, south of Khartoum on the Nile, and would get there well before Kitchener. Macdonald's instructions were to reach Fashoda first. The expedition's officers reached Mombasa in July 1897. After moving inland to a base camp at Ngara Nyuki, in September the force was divided into three columns. Captain Herbert H. Austin would lead 300 men north to uncover the source of the
Juba River, thought to be connected with
Lake Rudolph. The second column, under Macdonald, would go northwest to the Nile and then downstream to
Fashoda, arriving there before the French. A third column would supply the first two. However these plans were thrown into disarray when the escort of
Nubian troops from
Sudan deserted and fled to Lake Victoria. The Nubian troops had been the Egyptian garrison of
Equatoria in the south of Sudan under the leadership of
Emin Pasha. In 1885 they were threatened by the forces of
Muhammad Ahmad, the self-proclaimed
Mahdi whom Kitchener was now preparing to attack, and retreated south to Lake Albert. Emin was "rescued" in 1888 by
Henry Morton Stanley. With nowhere else to go, the Nubians had accepted the offer of Captain
Frederick Lugard to sign up with the British in 1891, but over the years they had accumulated many grievances. Macdonald spent the next seven months trying to suppress their mutiny, finally handing over responsibility for this task in May 1898 to troops that had been dispatched from India.After the mutiny was put down under the leadership of the Protectorate consul-general
George Wilson CB, Macdonald recommended retaining a force of Indians in the country on the basis that the Sudanese troops could be useful, but only if there was an independent body of sepoys. By the end of May 1898, Macdonald decided he did not have enough people or supplies to reach his original objective of Fashoda. Instead, his column would aim for
Lado, further south on the Nile, while Austin's column would pursue its original objective of exploring around
Lake Rudolf. On the route to Lado Macdonald's column passed through
Lotuko country in what is now the
Eastern Equatoria state of South Sudan, where he was given a friendly reception by the Lotuko chief Lomoro Xujang. Macdonald saw a resemblance between the
Maasai people and the Lotuko, and for this reason later recommended incorporation of the Lotuko lands into Uganda. Both of Macdonald's columns managed to return to Mombasa by December 1898, having completed their revised tasks, and the force was disbanded early in 1899. This was one of the last incidents in the
Scramble for Africa, in which almost the entire continent was brought under European rule. He was appointed a Companion of the
Order of the Bath (CB) in the
1900 New Year Honours list on 1 January 1900 (the order was gazetted on 16 January 1900), and invested by
Queen Victoria at
Windsor Castle on 1 March 1900. ==Interlude==