Lost Jerusalem was the name given to Earth in T.C. 0016. After the Immigrant Fleet left Lost Jerusalem, the planet suddenly vanished. Since the disappearance of Lost Jerusalem, the Galaxy Federation has moved its capital four times. The Ormus cult considers Lost Jerusalem to be a holy place, due to its history with the Zohar. There have been dozens of attempts to discover the ancient human capital. In the Proto Merkabah superfacility, there is a holographic starmap; chaos comments on a large "uncharted" hole where Lost Jerusalem was supposedly located.
A trailer for Episode III shows Shion finding herself on a portion of Lost Jerusalem's land in a ruined temple area. This portion is in fact Rennes-le-Château, which has been separated from Lost Jerusalem. At this time, Lost Jerusalem is revealed as the Planet Earth. Which is the Floating Landmass during game play
At the end of Episode III, after the credits, KOS-MOS' body is seen drifting towards the planet. This is where the series comes to a closure. Supposedly, the planet that KOS-MOS drifts to is Lost Jerusalem. And that Humanity had too start another Human Race and civilization on Lost Jerusalem.