As the war progressed, gradually the formation of carrier born squadrons and flying training became the principal task of the Daedalus Air Station. The wartime expansion included the present runways which were built in 1941 to 1942.  During this period, Grange airfield was used to train pilots and HMS Daedalus continued to house seaplanes and the Swordfish torpedo bombers involved in Channel Defences. Meanwhile, between 1942-45, revised training arrangements were put in place, and new entry naval training of observers and pilots were transferred from Lee-on-Solent to HMS St Vincent at nearby Gosport.

During this period, of the scores of aircrew who passed through HMS Daedalus, the two well known actors Lord Olivier and Sir Ralph Richardson served as pilots together during 1941-42, having just returned from making a series of films in the United States, including Wuthering Heights (1939), Rebecca (1939), and Pride and Prejudice (1940).

When England went to war, Olivier planned, like his good friend the actor David Niven, to join the RAF. But he could not get out of his contract. While sweating it out, he took flying lessons and, in an unusually short time, piled up 200 hours. In two years' military service Olivier became a lieutenant in the Fleet Air Arm. He stepped unhurt out of a number of forced or crash landings, gave ground and gunnery instruction, and never saw combat. But when he got back to work once more as an actor, theatrical London realized that a remarkable new artist had appeared. Olivier has no explanation for the change in himself except to say: "Maybe it's just that I've got older."

In 1941, Naval Air Squadron No. 811 based at RNAS Lee-on-Solent was the first and only squadron to receive Chesapeakes for operational service. On 28 March, 1940, the French government had placed an order for the American built Chesapeake, but they were not ready for delivery before France fell to the German advance, and the contract was taken over by the British and given to the Fleet Air Arm.  The Squadron received a total of 14 aircraft during July of 1941.  The aircraft remained on duty for only five months, and being regarded as obsolete were rapidly replaced by Fairey Swordfish aircraft in November, 1941. By May of 1944, the last Chesapeake was withdrawn from Fleet Air Arm service when Squadron No. 770 retired their last target-towing aircraft.

It was also at Lee-on-Solent that Lieutenant Commander Esmonde (posthumous VC)  and No. 825 torpedo bomber reconnaissance swordfish squadron was stationed prior to their heroic deeds to try and sink German capital ships in the English Channel. Esmonde and his squadron flew to Manston in Kent immediately before he led the ill fated Swordfish attack against the German Fleet consisting of the Gneisnau, Prinz Eugen, and Scharnhorst which were attempting a breakout in the Channel on 1 February 1942, dashing to return to Germany. All six Fleet Air Arm aircraft were lost in the attack and few crews survived. Esmonde was was to receive the posthumous VC, only one of two VCs won by the Fleet Air Arm in World War Two. A tribute to Esmonde can still be seen today at the Roman Catholic church at Lee.