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.
In August 2012, Travelocity faced a viral controversy when it offered a $200 coupon code to attendees at the National Federation of the Blind annual conference in Dallas. After the NFB posted the code on Twitter without mentioning the attendee restriction, Travelocity re-tweeted it without noticing the error but deleted the tweet a day later. After some travel blogs and message boards resposted the code, many ineligible travelers used the code. Travelocity responded by cancelling all trips that used the code who weren't on the list of attendees at the NFB annual conference. This resulted in a barrage of complaints from customers angry to see their trips suddenly cancelled.
Dave Siegel took the chief executive officer role in January 2012. Siegel's tenure ran through May 2015, when he left for personal reasons and was succeeded by the company's chairman, Bill Franke, who would manage strategy and finances. In April 2014, Barry L. Biffle was appointed as the company's president, reporting to Siegel; after Siegel's departure, Biffle was charged with managing the company's day-to-day operations.
The TWA Hotel is the TWA Flight Center structure currently being rebuilt as 505-room hotel, preserving the Eero Saarinen headhouse while replacing the structures on either side of the headhouse. Situated in front of JetBlue's JFK terminal, JetBlue has stated that it estimates the ownership of the hotel would be between 5–10% of the final total investment. The hotel will be an effective replacement for the Ramada Plaza JFK Hotel on the north end of the airport grounds in Building 144, which closed in 2009.
Also in 2010, JetBlue entered into interline booking agreements with South African Airways and American Airlines to facilitate luggage transfers between airlines for passengers with connecting flights on a different carrier. The agreement with American included JetBlue's 18 destinations not served by American and American's 12 international flights out of New York–JFK and Boston Logan. In addition, American gave JetBlue 8 round trips slots out of Washington National in D.C. and 2 out of Westchester, New York. In return, JetBlue gave American 6 round trips out of New York–JFK. The agreement with American Airlines has since ended according to JetBlue's website.
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After making a codeshare agreement with Lufthansa that went into effect in 2010, jetBlue transitioned to the Sabre reservation system used by Lufthansa, enabling the airlines to sell tickets on each other's flights, transfer luggage and passengers between the two carriers, and combine frequent flyer programs,. By making use of JetBlue's North America routes as a feeder network, the agreement put Lufthansa in a position to operate quasi-hubs in New York–JFK and Boston Logan.