Thomson buried his leader under a tree on which he carved Johnston's initials and the date of his death – 28 June 1879. He also attempted to climb Mount Hatambula, the highest mountain in the Selous National Park, and name it after Johnston, but the effort was aborted. This task was finally carried out in 2001 by James McCarthy, Johnston's biographer, and Mike Shand, senior cartographer from Glasgow University.
     Thomson successfully led the RGS team over 3,000 miles in 14 months, collecting many specimens and, on his return, writing the best-selling 'To the Central African Lakes and back'. He acknowledged his inexperience and lack of knowledge of surveying and the use of instruments but he wrote: 'I felt I must go forward, whatever might be my destiny. Was I not the countryman of Bruce, Park, Clapperton, Grant, Livingstone and (Lovett) Cameron?'
     In 1881, Thomson explored the Rovuma River valley in East Africa to search for coal for the Sultan of Zanzibar and, in 1883, he led another RGS expedition to explore a route from the eastern coast of Africa, through the hostile land of the Masai, to the northern shores of Lake Victoria, travelling through the Great Rift Valley. Thomson's expedition successfully demonstrated the feasibility of the route and made many biological, geological and ethnographic discoveries and observations. However, on the return journey, he was gored by a bull and subsequently suffered from malaria and dysentery. His heroic efforts, however, earned him the RGS's Founders' Medal on his return. By the following year, Thomson had recovered and was employed by the National African Company (later the Royal Niger Company), a mercantile company chartered by the government to help secure territorial rights in the lower Niger area. After this journey, Thomson returned in 1886 to lecture in the UK but was soon lured back to Africa on an expedition to the Atlas Mountains in 1888.
     In 1890, Thomson was employed by Cecil Rhodes to explore north of the Zambezi. This expedition was a bid to gain treaties and mining concessions from chiefs on behalf of the British South Africa Company, which had been chartered by the British government to claim the territory known as Zambezia (later, Rhodesia).
     During his various explorations, Thomson 'discovered' the Thomson Falls (Nyapuhura), sighted the Thomson's Gazelle (named after him and often simply known as the 'tommy'), was the first to understand the importance of the Rift Valley and was the first European to cross the Masai land. But his health had become severely compromised throughout his visits to Africa and he suffered from cystitis (inflammation of the bladder), pyelonephritis (inflammation of the kidneys) – both conditions caused by bacterial infections, and from schistosomiasis (a parasitic disease). Thomson sought various climates in which to recuperate, spending time in England, South Africa, Italy and France but he died in London of pneumonia on 2 August 1892.
     He never married, though his siblings produced 43 children between them. His legacy was his books. As well as 'To the Central African Lakes and back' (1881), Thomson wrote 'Through Masai Land' (1881), 'Travels in Africa and Southern Morocco' (1889) and a novel 'Ulu – an African Romance' (1888), together with his old school friend E. Harriet Smith. This tale concerns a disgruntled Scotsman named Gilmour who escapes from corrupt civilisation to the Kenyan highlands and is believed to be partly modelled on Thomson himself.

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