In 1999, USS "Theodore Roosevelt" departed for the Mediterranean and joined NATO forces for Operation Allied Force. VF-41's first strike was against an ammunition storage facility in Pristina, Kosovo on April 6. In July, "Theodore Roosevelt" was ordered to the Persian Gulf in support of Operation Southern Watch, where VF-41 became the first squadron to expend ordnance in two theatres on a single deployment. VF-41 logged over 1,100 combat hours during 384 sorties and dropped over 160 tons of laser-guided munitions with an unprecedented 85% success rate in support of Operation Allied Force and Operation Southern Watch.