In December 2016, a winter weather event disrupted fleet operations, causing Frontier to delay or cancel up to 70% of their flights during the peak of the crisis, many without any advance notice. On the weekend of December 17, the storm caused major delays at Frontier's Denver hub, and the effects of the storm were felt throughout the fleet. Flights were delayed or canceled at airports across the country, as in some cases, planes were ready to depart, but there were no rested flight crews available to service the flight. The head of Frontier's pilot's union issued a statement criticizing the companies' handling of the event, comparing the airline to a "house of cards". Frontier received over 30,000 refund requests for canceled flights resulting from the event.
On October 25, 2007, the airline opened a fourth focus city and operations base at Phoenix-Mesa Gateway Airport in Mesa, Arizona, connecting 13 cities already served by Allegiant and one new city to the Phoenix metropolitan area. The airport announced a 10,000-square-foot (930 m2) expansion in August 2008, which increased the number of gates from two to four and allowed Allegiant to triple the number of flights from Phoenix. The expansion was funded by a loan from Allegiant which will be repaid by passenger fees.
The initial JetExpress partnership with Mesa ended in January 2004, when Horizon Air was selected to operate the routes. Horizon utilized slightly larger CRJ-700 regional jet aircraft on these routes. In August 2006, Frontier and Horizon ended their partnership. While Frontier was generally pleased with Horizon's operation, the carrier decided that it needed to revisit the agreement and find a provider with additional regional jets to grow the operation. The last of the CRJ-700's was returned to the Horizon Air fleet on November 30, 2007.