2000s

On March 1, 2001, Continental launched non-stop service from Newark to Hong Kong, operating over the North circumpolar route. This service was the first non-stop long-haul route for any airline with flying duration exceeding 16 hours. The SARS outbreak in Asia caused service to be suspended until August 1, 2003. The launch in 2001 initiated a brief battle between Continental, United Airlines and Cathay Pacific over rights to non-stop flights between Hong Kong and New York. In 2003 non-stop daily services were started between Newark and Geneva, Switzerland and between Newark and Port of Spain, Trinidad and Tobago. On September 13, 2004 Continental entered SkyTeam alliance along with Northwest/KLM and CSA. Continental introduced new non-stop services to Oslo, Norway and Edinburgh, Scotland in 2004. In 2005, Continental expanded service from Newark to Beijing after being awarded the China route. During the same year, five new European destinations were added: Stockholm in Sweden, Belfast and Bristol in the United Kingdom, and Hamburg and Berlin in Germany. Services were added to Copenhagen, Denmark and Cologne, Germany in 2006, and to Athens, Greece in 2007. Among U.S. airlines, only Delta (with its extensive network of legacy routes dating from Delta's acquisition of Pan American's European network) serves more European destinations than Continental.

In 2005 service to Asia was expanded as Continental introduced daily nonstop service between Newark and New Delhi, India. The success of this Newark-New Delhi route presaged establishment of a second gateway in India with the announcement of daily nonstop service to Mumbai. With the establishment of Mumbai service, Continental offers the most nonstop flights by any carrier from the United States to India. By May 2006, the carrier's passenger traffic surpassed that of Northwest Airlines, and Continental became the fourth-largest U.S. carrier, the first change in the top-five passenger enplanement rankings since 2001. The Wall Street Journal reported on December 12, 2007 that Continental was in merger discussions with United Airlines. Of issue would be Continental's golden share held by Northwest Airlines, dating from a stakeholding relationship during the late 1990s, and the divestiture of Continental's Guamanian hub. A deal was not "certain or imminent", with the talks being of a preliminary nature. In April 2008, at the height of oil prices, Northwest announced a merger with Delta Air Lines. This allowed Continental to buy back the golden share from Northwest Airlines, which it did. Continental then renewed merger talks with United Airlines, but Continental ended the merger talks that same month.

In May 2008, Continental Airlines sold its remaining 4.38 million share investment in Panamanian flag carrier Copa for $35.75 a share, netting proceeds of $149.8 million. Continental had been a principal shareholder in Copa. In June 2008, due to national and international economic conditions, Continental cut 3,000 jobs and the CEO and president had reduced salaries for the remainder of the year. The airline also reduced capacity and eliminated 67 mainline aircraft from its fleet by the end of 2009, retiring all of Continental's 737-300s and all but 35 of its 737-500s. Continental also announced that it planned to withdraw from the SkyTeam Alliance and would join the Star Alliance in order to cooperate more extensively with United Airlines and other Star Alliance airlines. The new Continental-United relationship has been characterized as a "virtual merger" in some circles. Continental had maintained its SkyTeam affiliation to be business-as-usual until the day of withdrawal. Continental had been in discussions with United Airlines earlier in 2008 which might have resulted in a merger of the two carriers, but Continental withdrew from these discussions stating that it intended to continue to operate as presently constituted.

In September 2008, Continental announced that it would commence providing seasonal non-stop service between Houston and Rio de Janeiro. The new non-stop flight was timed to provide roundtrip flight connections at Continental's Houston hub to more than 160 cities throughout the U.S., Canada, Central America, Europe, and Asia. Continental renewed its lease for around 450,000 square feet (42,000 m2) in Continental Center I. Continental announced that its 4th quarter 2008 net loss widened to $266 million on costs for pilot retirement and reducing the value of its fuel hedges. In January 2009, Continental became the first commercial carrier to successfully demonstrate the use of sustainable biofuel to power an aircraft in North America. During the demonstration flight, Continental’s test pilots successfully conducted a number of flight maneuvers, and the biofuel met all performance requirements as compared with traditional jet fuel. The biofuel blend included components derived from algae and jatropha plants, both sustainable, second-generation sources that do not impact food crops or water resources or contribute to deforestation.[46] In March 2009, Continental became the first U.S. carrier to inaugurate scheduled service between New York and Shanghai, China, with daily non-stop flights from the airline’s hub at Newark Liberty International Airport.

In June 2009, Continental Airlines took delivery of another new Boeing 737-900ER, which was painted with a retro livery to commemorate the airline’s 75th anniversary. The new aircraft’s retro livery, which was originally used on aircraft beginning in 1947 and is called The Blue Skyway, was selected by Continental employees. Continental flew the aircraft to its three hubs for anniversary celebration events for employees and retirees. In July 2009 Continental began to offer DirecTV, giving customers the choice of 95 channels of live television programming, more channels than any other carrier. The channel lineup includes CBS, NBC, Fox, USA Network, Discovery Channel, A&E, CNN, ESPN, Animal Planet, The History Channel and many other popular channels. The fee for economy-class customers was $6 per flight. Continental also launched Virtual Expert technology on their website at continental.com, offering customers 24-hour support on the Web for all their travel needs. “Alex,” the airline’s Virtual Expert, interacts with customers to easily and effectively interpret requests and provide accurate answers to travel needs. Continental was the first airline to use this technology.[50] Continental Airlines joined Star Alliance on October 27, 2009, initiated with a closer partnership with United Airlines. Continental’s transition to Star Alliance is a strategic change that will enhance travel options and competition. Continental’s network will have a distinct fit in Star Alliance, with Continental’s New York hub at Newark Liberty International Airport playing a particularly important role for Star Alliance travelers.

Continental Airlines began new non-stop service from its Houston hub to Edmonton International Airport beginning November 1, 2009, subject to government approval. The daily flight was the 11th Canadian destination to be served by Continental and the fourth Canadian destination from the airlines’ Houston hub.[52] Continental also started service from its hubs at Houston and Cleveland to Washington Dulles International Airport (IAD). Continental Airlines also launched daily nonstop service between its Houston hub at Bush Intercontinental Airport and Frankfurt on November 1, 2009, subject to government approval. Frankfurt is the airline's fourth European city served directly from Houston. The airline had already been operating daily flights to Frankfurt from its New York hub at Newark Liberty International Airport. In December 18, 2009, Continental began new service from its Guam hub and Honolulu to Nadi, Fiji. The service was to be operated by Continental Micronesia.