Linnell joined the Royal Naval Reserve as temporary warrant-telegraphist in September 1914, serving with the Royal Naval Air Service in France and Belgium. He learnt to fly at the Grahame-White Flying School Hendon. Flying a Grahame-White Biplane he gained Royal Aero Club Certificate No.1338 in June 1915. Flt Sub-Lt Linnell was responsible for carrying out trials in a special Blackburn-built B.E.2c. The unique aircraft No.3999 was ordered by Admiralty for W/T experiments, it was fitted with a 70 hp Renault engine and had a top speed of 72 mph. Blackburn-built B.E.2cs are recognisable by the ringed airscrew motif on the fin and saw active service in every theatre during the war. From March 1916 till the end of 1919 he served with the Grand Fleet as a pilot on, and and was mentioned in despatches twice. He ended the Great War with a permanent commission of captain in the newly formed Royal Air Force. The Dunning Memorial Cup, given annually to the officer that has done the most to further aviation in connection with the fleet, was awarded Linnell in 1920 "... for flights which led to important developments in artillery and reconnaissance observation."
Inter war years
From 1920 he worked as a Royal Air Force Communications Officer at the Department of Civil Aviation, then transferred to Signals Staff duties at the Air Ministry in 1925. He was appointed an Officer of the Order of the British Empire in June 1923, the citation reads, "This officer has done exceptionally good work in connection with Signals. His liaison with the Navy and the Army has been excellent." He received special thanks from the Air Council for preparing the handbook on air communications and intelligence systems for the air defence of Great Britain. His first command on 20 October 1930 was No. 9 Squadron RAF located at RAF Manston and then in September 1931 Wg Cdr Linnell was Officer Commanding RAF Malta. He spent 1933 attending the course at RN Staff CollegeGreenwich after which he took command of No. 99 Squadron RAF He became the first Station Commander at RAF Mildenhall four days before it hosted 70,000 people for the start of the RAeCMacRobertson Air Race of 1934. Then in July 1935, the year of the Silver Jubilee, RAF Mildenhall welcomed King George V for the first ever Royal review of the RAF. Linnell returned to the Air Ministry in July 1935 as Deputy Director of Organisation, Department of A.M.S.O.
Linnell was apparently against the idea of a bouncing bomb reasoning that it was drawing development resources away from the prototype high altitude bomber Vickers Windsor, his thinking may have been influenced by Charles Craven, the Chairman at Vickers. Early in 1943, tests authorised by Linnell in June 1942 at the instigation of Sir Henry Tizard, indicated that a bouncing bomb was technically feasible. A meeting between the Air Ministry, RAF Bomber Command and MAP decided to continue development of project Upkeep with a proposal to have a fully trained squadron ready by May. AOC-in-C of RAF Bomber Command Harris thought differently and saw the project as a waste of precious Lancasters. However Chief of the Air StaffPortal was convinced by film footage of the tests and ordered three Lancasters allocated to the project. One week later, at a meeting convened by Linnell, the number of Lancasters ordered had risen to a squadron and Operation Chastise was planned for that spring.