Cottesmore, before the end of the crisis on 8 October saw the squadron return to 1 Group and Eastchurch. On 1 January 1939, the squadron rejoined 2 Group, and moved to RAF Watton in Norfolk on 2 March 1939. On the outbreak of the Second World War, the squadron was converting to the Blenheim IV and so was not fully operational, mainly flying reconnaissance missions. In May 1940, during the Battle of France it began daylight attacks on advancing German columns in the Low Countries and France, flying its first mission of the campaign on 11 May, when 11 Blenheims attacked a bridge at Maastricht for no result except for two Blenheims shot down and eight damaged. From June to October 1940 the squadron operated from RAF Lossiemouth in Scotland to attack German shipping off the coast of Norway and to deter any German invasion across the North Sea. Back in Norfolk the squadron began regular low-level attacks on enemy shipping. On 26 April, a detachment of six Blenheims from 21 Squadron was detached to Malta in April 1941, serving there until May. The operation was considered successful, and as a result squadrons of 2 Group were regularly despatched to Malta, operating there for about five weeks before ferrying the aircraft to North Africa, with some pilots returning home and some remaining in theatre. At the end of 1941 the squadron again moved to Malta to attack Italian shipping and targets in Italy and Libya. By this time Malta was under heavy air attack and the squadron took heavy losses both during combat (with landing back at Malta becoming increasingly dangerous owing to the heavy presence of enemy fighters), and owing to bombing of the aircraft on the ground at RAF Luqa. The squadron was disbanded in Malta on 14 March 1942. On the same day a new 21 Squadron was formed at RAF Bodney, still with the Blenheim, but re-equipped a few months later with the Lockheed Ventura. It was the first RAF squadron to use the Ventura, moving to RAF Methwold on 1 November. It flew its first operational mission using the Ventura, a low-level attack by three aircraft on railway lines near Hengelo in the Netherlands, on 3 November. On 6 December it took part in Operation Oyster, a large-scale attack by 2 Group on the Philips works at Eindhoven, with three of its aircraft being lost.