Flagship Airlines traced its origins to Air Virginia, a commuter and regional feeder air carrier, which later changed names to AVAir. AVAir had rapidly declined into bankruptcy following the AVAir Flight 3378 tragedy. AMR Corporation founded Nashville Eagle out of the assets of AVAir. Flagship Airlines was formed by the merger of Command Airways into Nashville Eagle.
The airline operated for American Airlines under the American Eagle brand name. Flagship flew British Aerospace BAe Jetstream 31 commuter turboprop aircraft and provided passenger feeder service via a code sharing agreement for American Airlines which formerly operated a hub at the Nashville International Airport.
Ultimately, Flagship Airlines merged with Simmons Airlines to form American Eagle Airlines (now Envoy Air) and the former Simmons IATA two letter code of MQ became the surviving identifier for the unified airlines.
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