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Turnaround
In 1998, Jonathan Ornstein was appointed CEO of Mesa Air Group. Ornstein had been Risley's assistant from 1989 to 1995 during Mesa's initial expansion. Larry Risley remained on Mesa's board of directors. All corporate officers were replaced and the company headquarters was relocated from Farmington to Phoenix. The flight training and human resources departments were also moved to Phoenix. Its plan to return to profitability focused on several fronts: its aircraft, its codeshares, and customer service
One of Mesa's problems during the turnaround was that it operated over 180 turboprops. It began consolidating all of its remaining Beechcraft 1900 turboprops into Air Midwest, completing the consolidation in 2000. It embarked on a plan to reequip with jet aircraft. In 1999, Mesa arranged to purchase 36 Embraer 145 jets with options for 64 additional ERJs. In 2001, Mesa arranged to purchase 20 CRJ-700s and 20 CRJ-900s with options for 80 additional CRJ-700/900s. Five of the CRJ-700 orders were subsequently converted to CRJ-900s. As Mesa took delivery of the larger CRJ-700s and CRJ-900s, scope restrictions with US Airways prevented Mesa from operating the larger aircraft in its Mesa Airlines subsidiary. Mesa created a separate subsidiary, called Freedom Airlines to operate these aircraft. As the scope restriction at US Airways was removed during US Airways' bankruptcy reorganization and after Mesa settled with its pilot union regarding operating Freedom as a separate air carrier, Freedom's aircraft and pilots were merged back into Mesa Airlines in 2003.
As Mesa completed its restructuring, it proceeded to reestablish it codeshares. In 1998, it negotiated a new codeshare with America West and expanded its codeshare with USAir. In 2001, Mesa reestablished a codeshare agreement with Midwest Express for its Air Midwest Kansas City hub. Also that same year, Mesa negotiated an agreement with Frontier to operate as Frontier JetExpress out of Denver. The Frontier codeshare ended in 2003. In 2003, Mesa reestablished a codeshare agreement with United, operating as United Express. In 2005, Mesa negotiated a codeshare agreement with Delta for Freedom Airlines to operate as a Delta Connection carrier.
By 1999, Mesa returned to profitability. Mesa acquired CCAir and its USAir Express codeshare in 1999. It continued to operate CCAir as a separate operation. By 2002, CCAir ceased operations due to high costs and its assets and employees were absorbed into Mesa. The latest merger attempt was in 2003, when Mesa offered to acquire Atlantic Coast Airlines. Its offer was refused, and ACA went on to operate independently as Independence Air and later ceased operations in January, 2006. In 2006, Mesa began operating in Hawaii under the brand go! and established a codeshare agreement with Mokulele Airlines, where Mokulele will operate as a go! Express carrier.