AMR Corporation founded Nashville Eagle out of the assets of AVAir and Air Midwest.
Flagship Airlines was formed by the merger of Command Airways into Nashville Eagle on June 1, 1991.
The airline served the East Coast and the Bahamas from hubs at Miami, Nashville, New York-JFK, and Raleigh/Durham.
The former Simmons IATA two letter code of MQ became the surviving identifier for the unified airlines.
On 13 December 1994, Flagship Airlines Flight 3379, operating for American Eagle, entered an aerodynamic stall and crashed into a wooded area during a missed approach to Raleigh–Durham International Airport in North Carolina.