The Flagship Program is a series of NASA missions to explore the Solar System. It is the largest and most expensive of three classes of NASA Solar System Programs – the other two being the Discovery Program, which is the cheapest in cost, and the New Frontiers Program, which is medium-cost.
According to NASA, the cost of Flagship Program missions ranges between $2 billion and $3 billion. These missions will be crucial in allowing humans to reach and explore high-priority targets. These critically important targets could help establish the limits of planetary habitability, not just for our Solar System, but for planetary systems in general. In particular, they potentially provide an opportunity to identify pre-biotic organic molecules or even extant life beyond Earth, should it exist, in the Solar System. The targets of Flagship Missions may include complex missions to the clouds and surface of Venus, the lower atmosphere and surface of Titan, the surface and subsurface of Europa, the deep atmosphere of Neptune, the surface of its moon Triton, and the surface of a comet nucleus in the form of cryogenically preserved samples.
The flagship program includes the Mars Science Laboratory, the Cassini spacecraft, the Galileo spacecraft, and the Voyager probes. The Voyager probes mark the transition between the original NASA unmanned mission programs, which were funded and organized as a series of related missions to specific targets such as the Mariner probes, Viking landers, Pioneer probes, Surveyor landers, Ranger satellites, etc. and the modern NASA program which includes flagships. In the early 1990s, NASA made the decision that instead of a centrally planned mission approach around pre-selected targets, mission ideas would be competed. The competitions would be based in cost categories, eventually turning into the Discovery, New Frontiers, and Flagship program. While teams self-assemble to compete for Discovery and New Frontiers missions, Flagship programs are still strongly influenced by NASA headquarters. Also, Discovery and New Frontiers missions are scheduled frequently enough that a standard process has emerged and scientists can expect that process to be followed, but Flagship programs seem to follow a different organizational and development approach every time.
The 2011 Planetary Science Decadal Survey report recommended to NASA that the highest priority flagship mission for development was a sample-caching rover, called the Mars Astrobiology Explorer-Cacher (MAX-C), as an American contribution to the ExoMars program with the European Space Agency (ESA) and as precursor to a proposed Mars sample return mission. The second highest priority mission was identified as the Jupiter Europa Orbiter, proposed to be part of the NASA-ESA EJSM/Laplace mission, and would have studied Europa in detail as a site of astrobiological interest.
Current status 
Under the FY2013 budget that President Obama released on February 13, 2012, NASA terminated its participation in ExoMars due to budgetary cuts, in order to pay for the cost overruns of the James Webb Space Telescope. In addition, all proposed NASA flagship planetary missions were put on hold indefinitely. As of March 2012, there are no plans to develop more planetary flagships beyond the $2.5 billion Mars Science Laboratory (MSL).
See also 
- Visions and Voyages for Planetary Science 2013 - 2022 (Published in 19 October 2011)
- New approach for L-class mission candidates. ESA - 19 April 2011
- "Lean U.S. missions to Mars, Jupiter moon recommended". 7 March 2011 (Reuters). 8 March 2011.
-  Aviation Week (February 14, 2012)
- "Experts React to Obama Slash to NASA’s Mars and Planetary Science Exploration". Universe Today. February 1, 2012. Retrieved 2012-02-18.
- NASA Flagship Planetary Missions on Hold Indefinitely
- "NASA shelves ambitious — and expensive — flagship missions"