Waddington's colleague Patrick Blackett, Scientific Adviser to Coastal Command, established the Operational Research Group. In March 1943 Waddington was appointed Deputy Officer-in-Charge of the Operational Research Section, a position which he held during the anti U-Boat campaign of that year. In October he was promoted to Principal Scientific Officer and in December Officer-in-Charge and Scientific Adviser to the Commander-in-Chief, Coastal Command, dealing with photographic reconnaissance and anti-shipping strikes. Waddington wrote the Coastal Command chapter in Operational research in the R.A.F, which was, however, not published until 1963. His own monograph, Operational Research In World War II: O.R. against the U-Boat, was eventually published by Elek Books, London, in 1973.