The bankruptcy allowed Maurice J. Gallagher Jr., one of the airline's major creditors, to gain control of the business. A veteran leader of low-cost airlines, Gallagher had worked with WestAir and as CEO of ValuJet Airlines. In June 2001, Gallagher restructured Allegiant to a low-cost model, focusing on smaller markets that larger airlines did not serve with mainline aircraft. Allegiant's headquarters and operations were also moved to Las Vegas.
jetBlue experienced its first-ever quarterly loss during the fourth quarter of 2005 when the airline lost $42.4 million, enough to make them unprofitable for the entire year of 2005. The loss was the airline's first since going public in 2002. JetBlue also reported a loss in the first quarter of 2006. In addition to that, jetBlue forecasted a loss for 2006, citing high fuel prices, operating inefficiency, and fleet costs. During the first quarter report, CEO David Neeleman, President Dave Barger, and then-CFO John Owen released JetBlue's "Return to Profitability" ("RTP") plan, stating in detail how they would curtail costs and improve revenue to regain profitability. The plan called for $50 million in annual cost cuts and a push to boost revenue by $30 million. jetBlue Airways moved out of the red during the second quarter of 2006, beating Wall Street expectations by announcing a net profit of $14 million. That result was flat when compared to jetBlue's results from the same quarter a year before ($13 million), but it was double Wall Street forecasts of a $7 million profit, Reuters reports. The carrier said cost-cutting and stronger revenue helped it offset higher jet fuel costs. In October 2006, jetBlue announced a net loss of $500,000 for Quarter 3, and a plan to regain that loss by deferring some of their E190 deliveries and by selling 5 of their A320s.
In May 2017, Allegiant Air took delivery of its first brand-new A320. Allegiant took delivery of ten new A320s in 2017 and is scheduled to accept two in 2018. All new aircraft will be painted in Allegiant's new livery at the time it is delivered. Older Airbus aircraft will be repainted during their C-checks. The new Airbus aircraft will have fuel-efficient sharklets. The new A320s seat 186 passengers, an increase of the 177 seats that are found in the rest of the Allegiant A320 fleet. To fit the additional nine seats, Allegiant opted for the Airbus Space-Flex V2 Lavatory. 
Allegiant also earns commissions by offering hotel rooms, car rentals and admission to tourist attractions on its website. It sells package vacations under the brand name Allegiant Vacations. The company has arrangements with 34 hotels in Las Vegas and 21 in the Orlando and Daytona Beach, Florida, areas. In 2008, the airline sold 400,000 hotel room nights. Commissions on hotel and rental car packages are up to one-third of the airline's revenue.
On October 22, 2008, jetBlue opened its new primary hub at John F. Kennedy International Airport (JFK), Terminal 5, or simply T5. The mostly new terminal, costing approximately $800 million, partially encircles the historic TWA Flight Center, the former Trans World Airlines terminal designed by Eero Saarinen, which remains closed. According to the plan, passengers will eventually be able to check in for flights in the landmark building, then transfer to the new structure via the original passenger departing-arrival tubes from Saarinen's original terminal and its 1969 addition by Roche-Dinkeloo.
In 1997, Maverick Airways was operating code share service for Frontier with de Havilland Canada DHC-7 Dash 7 STOL capable turboprops between Denver (DEN) and two destinations in Colorado: Grand Junction (GJT) and Steamboat Springs (SBS). However, the service was short lived as Maverick encountered financial challenges and then ceased all flights.
Allegiant Air has been closely monitored by the FAA due to many emergency landings and aborted takeoffs. ABC interviewed a former Allegiant mechanic, who said "Dedicated steps were not being performed with maintenance manuals or even with general practices, before an aircraft is released." Many of these incidents had involved Allegiant's aging MD-80 aircraft, which as of November 2018 have been replaced by newer Airbus A320 family aircraft. 46 of the 86 aircraft have made emergency landings, all of which were on MD-80s. The average age of Allegiant's MD-80 fleet was 29 years compared to less than 13 years for its Airbus fleet.
On June 22, 2009, Frontier Airlines announced that pending bankruptcy court approval, Republic Airways Holdings, the Indianapolis-based parent company of Republic Airlines, would acquire all assets of Frontier Airlines for the amount of $108 million. Thus, Frontier Airlines would become a wholly owned subsidiary of Republic. However, 5 weeks later on July 30, Dallas-based Southwest Airlines announced that it would be making a competing bid of $113.6 million for Frontier with intentions to also operate Frontier as a wholly owned subsidiary, but that it would gradually fold Frontier resources into current Southwest operating assets.
On March 22, 2010, jetBlue announced it would remain in the New York City area, in Long Island City, because of the airline's historical links to the city, the cost of staff relocations, the airline's desire to retain access to financial markets, and because Aer Lingus and Lufthansa, jetBlue's marketing partners, fly into JFK Airport. jetBlue planned to combine its Forest Hills and Darien, Connecticut offices, together about 1,000 employees, into about 200,000 square feet (19,000 m2) in the Brewster Building by mid-2012.
In 2007, jetBlue was also facing reliability problems with its Embraer 190 fleet. For a couple of months, jetBlue contracted ExpressJet to operate four Embraer 145 regional jets on behalf of jetBlue. While this was going on two E-190 aircraft at a time were sent to an Embraer maintenance facility in Nashville, Tennessee. ExpressJet operated routes between Boston Logan and Buffalo, New York and Washington Dulles, and between New York–JFK and Columbus, Ohio (has terminated) and Richmond, Virginia.