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The observatory has worked far longer than expected, but its supply of liquid helium finally depleted at 22:11 UT May 15, 2009, nearly six years after launch. At that point, mission scientists reconfigured the mission as the Spitzer Warm Mission, which would use the two shortest-wavelength modules of the infrared array camera (IRAC), which did not require the cryogenic helium to operate, for future observations.

More discoveries followed. In August 2010, data from Spitzer revealed the identification of the first carbon-rich planet (known as WASP-12b) orbiting a star. In October 2012, astronomers announced that data from the observatory had allowed more precise measurement of the Hubble constant, the rate at which the universe is stretching apart.

The following year, Spitzer celebrated 10 full years of operation in space and continued operation of its two instruments which, in August 2014, observed an eruption of dust around a star (NGC 2547-ID8), possibly caused by a collision of large asteroids. Such impacts are thought to lead to the formation of planets.

Continuing discoveries based on results from Spitzer (as well as data integrated with information from other space-based observatories such as Swift) were announced in April 2015 (discovery of one of the most distant planets ever identified, about 13,000 light-years from Earth) and in March 2016 (discovery of the most remote galaxy ever detected, a high-redshift galaxy known as GN-z11). The latter was detected as part of the Frontiers Field project that combines the power of Spitzer, Hubble and Chandra.

In August 2016, mission planners at NASA's Jet Propulsion Laboratory (JPL) announced a new phase of the mission known as “Spitzer Beyond,” leveraged on a two-and-a-half-year mission extension granted by NASA earlier in the year.

Because the distance between Spitzer and Earth has widened over time, the telescope’s antenna must be pointed at higher angles toward the Sun to communicate with Earth. As a result, parts of the spacecraft will experience increasing amounts of heat. Simultaneously, its solar panels will be pointed away from the Sun in this configuration, thus putting onboard batteries under more stress. These challenges will be a part of the Spitzer Beyond phase.

In February 2017, NASA announced that Spitzer had revealed the first known system of seven Earth-size planets around a single star. Three of the planets are firmly located in the habitable zone, the area around the parent star where a rocky planet is most likely to have liquid water. The discovery set a record for the greatest number of habitable-zone planets found around a single star outside our solar system.

In October 2017, NASA announced that it was seeking information from potential funders who might be able to support operation of the telescope after NASA funding runs out.

In August 2018, Spitzer marked 15 years in operation.