Omaha moved to the Continental Football League for the 1968 season and finished 7–5 in the Central Division. In September 1968, Glen Hepburn, a two-way player for the Mustangs, died from injuries sustained in a game.[3]
On December 15, 1969, the COFL revoked Omaha's franchise for failure to meet the league's financial obligations.[4] The league itself quietly disbanded after the 1969 season and the Mustangs joined the Trans-American Football League for the 1970 season.
In February 1971 the Mustangs announced they would be joining the Midwest Professional Football League.[5] The Mustangs did not operate for the 1973 season. They were revived as a fully independent team in 1974.