1998, the squadron took part in Operation Desert Fox, the four-day air campaign against Iraq. Deployments to the Persian Gulf continued, flying the upgraded Tornado GR4 from 2001, and included major contributions in 2003 as part of Operation Telic as well as supporting the first free elections in Iraq for 50 years in January 2005. In 2006 and again in 2008, No. 12 (B) Squadron provided armed overwatch for UK and US ground operations in Iraq. Shortly afterwards, as British troops withdrew from the country, the Tornado fleet based in the region also returned to the UK, marking the end of a long era of the aircraft in theatre. Between 6 to 16 October 2008, the squadron deployed to RAF Fairford, Gloucestershire, to participate in Exercise Crown Condor alongside Saab JAS 39 Gripens from the Blekinge Wing of the Swedish Air Force. In June 2009, the squadron deployed ten jets to RAF Akrotiri, Cyprus, eight of which continued to Kandahar in Afghanistan. This marked the start of Tornado GR4 operations in Afghanistan, with the type replacing the Harrier GR9 in theatre. For over four months, No. 12 (B) Squadron successfully provided support to the International Security Assistance Force (ISAF), including close air support for, amongst others, British, American, Canadian and Afghan troops in all parts of the country. On 16 October 2009, No. 12 (B) Squadron returned to Lossiemouth after having handed over to a Marham-based GR4 squadron. Between subsequent Operation Herrick deployments during 2011, No. 12 (B) Squadron was deployed in support of Operation Ellamy, the UK’s participation in the military intervention in Libya under United Nations Security Council Resolution 1973. This saw ten aircrew deploy to Gioia del Colle in southern Italy to bolster the Tornado component during the peak of operations. The remainder of the squadron was held at readiness to move to RAF Marham to launch Storm Shadow raids on hardened Libyan targets. These missions required three air-to-air refuelling brackets on the outward journey and one further on return to Gioia Del Colle. No. 12 (B) Squadron carried out their last tour of Afghanistan from July to October 2013, being replaced by No. 617 Squadron. The squadron disbanded on 31 March 2014 under the command of Wing Commander Simon Strasdin. All Tornado aircraft were due to be withdrawn from RAF operations by the end of 2015. Consequently, No. II (AC) Squadron was expected to stand down