Six of No. 36 Squadron's Hercules evacuated over 450 civilians from Cambodia following the coup in July 1997. The unit again became responsible for its own routine maintenance in 1998, when No. 486 Squadron was disbanded. A detachment from No. 36 Squadron supported INTERFET operations in East Timor between September 1999 and February 2000. The squadron was assigned four C-130Es previously operated by No. 37 Squadron during the latter's transition to the new C-130J Super Hercules, which commenced in 1999; the E models were retired the following year. No. 36 Squadron was once more awarded the Gloucester Cup in 2001. It took part in relief efforts following the Bali Bombings in October 2002. In February 2003, it deployed a detachment of two Hercules to the Middle East as part of the Australian contribution to the invasion of Iraq. The aircraft arrived on 10 February, and began flying transport sorties less than two weeks later. A No. 36 Squadron Hercules became the first Coalition aircraft to land at Al Asad Airbase, west of Baghdad, after it was secured by Australian special forces personnel. One aircraft was hit by ground fire near Baghdad on 27 June 2004, killing a coalition passenger. The detachment remained in Iraq until September 2004, when it was relieved by two C-130Js from No. 37 Squadron. No. 36 Squadron also participated in Operation Sumatra Assist in the wake of the 2004 Boxing Day tsunami.