During December 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 Air Force Wing of the Swedish Air Force.