The Flying saucer is an alien spacecraft buried beneath Gravity Falls, Oregon, apparently having crashed millions of years prior to the present day, it is responsible for the odd appearance of the Gravity Falls cliffs. Ford Pines is uncertain whether the saucer is responsible for the Anomalous Phenomena in Gravity Falls, or rather that the presence of the phenomena is what drew the craft there to begin with.
Ford discovered the existence of the saucer some time after arriving in Gravity Falls, and he and his partner Fiddleford McGucket scavenged materials from it for use in their universe portal and other projects. Due to the ship having crashed millions of years ago, the passengers and crew were long dead, as well as most of the systems. In addition to collecting parts, the two geniuses spent time studying the aliens' technology and language.
In "Dipper and Mabel vs. the Future," Ford reenters the saucer with Dipper after recounting its history in order to locate a powerful adhesive needed to repair the container holding the interdimensional rift. While they succeeded in locating it, they inadvertently activated one of the ship's long-dormant security systems. Ford was taken captive by a security droid and sent flying towards space, bound for an intergalactic prison, but was fortunately saved by the quick actions of Dipper.