In 1941 he was seconded to Special Operations, War Office, in 1941. In May 1943 he has parachuted into Montenegro as representative of the British GHQ in the Middle East to the central command of the Yugoslav Partisans, who were led by Josip Broz Tito. Deakin's mission, codenamed Typical joined Tito as the partisans were being hunted through the mountainous ravines of the region surrounding Mount Durmitor by German and Italian forces. Just below the summit of Mount Ozren, the partisans were trapped by German aerial bombardment and forced to take cover among birch groves. In one attack, a cluster of bombs fell among them, killing Deakin's radio operator, Bill Stuart, Tito's Alsatian dog, 'Maks', and wounding both Tito and Deakin.
The Operation Typical group were disbanded at the end of September 1943 and absorbed into the mission of Sir Fitzroy Maclean. Deakin's impressive reporting on the situation from on the ground is considered to have had a decisive impact on British policy towards the support of resistance movements in Yugoslavia (although the significant role of intelligence decrypts was not revealed until the 1970s, see Yugoslavia and the Allies).
He was assigned the role of Literary Assistant to Sir Winston Churchill during the years 1936-40, and the period 1945-55. He was described by Churchill's biographer, Sir Martin Gilbert, as being "at the centre of the web of all Churchill's literary efforts."
Subsequently, Deakin completed several historical works, drawing upon his experiences during both the Second World War and his time with Churchill. His publications include numerous articles on Yugoslavia, as well as The Brutal Friendship, published in 1962. The latter was a detailed examination of German-Italian relations during World War II, and revealed Deakin not only as a formidable historian of diplomacy, but also, in his assessment of the death of Italian fascism, a notable political analyst. He was later editor, with his friend Alan Bullock, of two series of historical texts, The British Political Tradition and The Oxford History of Modern Europe.
In 1950, he was appointed as the first Warden (or principal) of the new St Antony's College, Oxford. He remained in this role until 1968, when he was succeeded by another historian, Raymond Carr, who had been appointed as his Sub-Warden in 1966.
In 1963 Deakin returned to Montenegro to perform research for his wartime memoir of fighting with Tito's army. His memoir was published as The Embattled Mountain the title referring to Mount Durmitor, the environs of which Deakin and Tito's army had been pursued over by German and Italian forces; see Battle of the Sutjeska.
See also 
- Sir Fitzroy Maclean
- Special Operations Executive
- Winston Churchill
- Josip Broz
- Partisans (Yugoslavia)
- Yugoslavia and the Allies
- Atomic bomb
- Deakin, F.W.D. (1971). The Embattled Mountain. p. 1.
- Deakin, F.W.D. (1971). The Embattled Mountain. p. 18.
- Deakin, F.W.D. (1971). The Embattled Mountain. p. 265.
- Deakin, F.W.D. (1971). The Embattled Mountain. p. 80.
- Much of this research, as well as paperwork from his time as Literary Assistant to Winston Churchill, is held at the Churchill Archives Centre in Cambridge, and is accessible to the public. See the catalogue description for The Papers of Sir William Deakin.
- Deakin, F.W.D. (1971). The Embattled Mountain. p. 266.
- Deakin, F.W.D. (1971). The Embattled Mountain. Oxford University Press, London. ISBN 0-19-215175-4.
- Deakin, F.W.D. (1962). The Brutal Friendship: Mussolini, Hitler and the fall of Italian fascism. Weidenfeld and Nicolson, London & Harper and Rowe, New York.
- Obituary in The Times
- Eintrag "Deakin, Sir William" in Munzinger Online/Personen - Internationales Biographisches Archiv, URL: http://www.munzinger.de/document/00000010205 (German)