The airline also stated that a long term increase in the cost of fuel had prevented the operation from being profitable.

[8] In a memo explaining his decision to rule against Hawaiian's request for a preliminary injunction, U.S. Bankruptcy Judge Robert Faris wrote that e-mail made public during Hawaiian Airlines lawsuit raised "real doubts about the propriety of Mesa's conduct.

[10] Faris dismissed the counter suit on December 8, 2006, and at that time set an opening trial date on September 25, 2007.

Citing record high fuel prices and inter-island competition with Go!, it ceased passenger operation 11 days later.

[14] Hawaiian contended that Murnane deleted the files maliciously in an attempt to destroy evidence that would show that Mesa improperly used confidential data.

Mesa contended that Murnane accidentally deleted the files in question in an attempt to remove pornographic material from his computer.

[16] Faris, however, deferred any decision on damages pending the outcome of the trial, saying it still needed to be decided whether the information existed in the public domain.

[18] Following the ruling, Mesa requested a retrial claiming it had recovered the previously lost evidence on a third hard drive.

On December 13, Faris denied the request on the basis that new evidence would likely not change the outcome of the trial, and the airline planned to proceed with its appeal of the decision to US District Court.

[19] On April 30, 2008, the two airlines announced a settlement had been reached whereby Mesa would withdraw its appeal of the judgment and would pay Hawaiian $52.5 million.

[22] On March 3, 2009, bankruptcy judge Lloyd King blocked the sale of Aloha's name and brand on the grounds that the auction was not public and must be reheld.

[24] In October 2009, Mesa Air Group and Republic Airways Holdings merged their competing subsidiaries, Go!

Embraer 170 aircraft, operated on behalf of Mokulele by Republic subsidiary Shuttle America, were removed from Hawaii service.

During the concluding months of 2011 it was announced the complete divestiture of the Mokulele Airlines turboprop operations from Mesa Air Group's joint venture with Republic Airways Holdings.

Flight 1002 on February 13, 2008, overshot Hilo Airport by 30 miles (26 nmi; 48 km),[27] remaining 21,000 feet (6,401 m) in the air as it missed the destination.

Air traffic controllers were unable to reach the two pilots for 25 minutes, after which contact was re-established and the aircraft returned for a safe landing in Hilo.