In September 2006, the airline announced that it had reached an agreement with Mokulele Airlines, whereby Mokulele would operate Cessna Grand Caravan aircraft to Kapalua, Molokai, and Lanai under the name go!Express. Service began with flights from Kapalua to Honolulu, Kahului, and Kona on April 17, 2007. Service began for flights to Molokai on July 21, 2007 and flights to Lanai on October 06, 2007.
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 "raises real doubts about the propriety of Mesa's conduct.
In March 2006, Mesa filed a counter suit, claiming that Hawaiian was violating antitrust law by trying to keep Mesa out of Hawaii, using legal maneuvers to prevent Mesa from offering fares below the prevailing fares offered by Hawaiian. Mesa also alleged that Hawaiian had coerced two freight forwarders into refusing parts and equipment Mesa wanted to ship to Hawaii for the new airline. Faris dismissed the counter suit on December 8, 2006, and at that time set an opening trial date on September 25, 2007.
In October 2006, Aloha Airlines parent Aloha Airgroup filed a lawsuit similar to Hawaiian's, claiming that Mesa received confidential information during Aloha's Chapter 11 bankruptcy proceedings and improperly used it to enter the Hawaii inter-island market with the intent of driving Aloha out of business.
On March 20, 2008, Aloha Airlines filed for Chapter 11 bankruptcy protection. Citing record high fuel prices and inter-island competition with go!, it ceased passenger operation 11 days later.
As the trial date approached, it became known that Mesa's chief financial officer, George "Peter" Murnane III, had e-mailed an acquaintance about a week after Hawaiian filed suit, first asking for information about how to delete files in such a way that they could not be discovered, then confirming that the files in question were deleted. Mesa placed Murnane on paid administrative leave on September 22, 2007. 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.
On September 27, in a pretrial hearing, Faris preliminarily ruled that Mesa had misused confidential information in setting up go!, and failed to return or destroy confidential data acquired during the bankruptcy proceedings. "The misuse was a substantial factor in Mesa's decision on entering the Hawaii market," said Faris. 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. Following the hearing which lasted from September 28 to October 4, Faris ruled on October 30th that Mesa had misused the confidential information and ordered Mesa to pay Hawaiian $80 million, while rejecting Hawaiian's request to bar go! from selling tickets for one year. Following the ruling, Mesa requested a retrial claiming it had recovered the previously-lost evidence on a third hard drive. On December 13th, Faris denied the request on the basis that new evidence wouldn't likely change the outcome of the trial, and the airline plans to proceed with its appeal of the decision to US District Court. On April 30, 2008, the two airlines announced a settlement had been reached whereby Mesa would withdraw its appeal of the judgement and would pay Hawaiian $52.5 million.
As of April 2007, go!'s average fleet age was 7 years old.