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. And also, Lost Jerusalem has been revealed as the Planet Earth.

At the end of Episode III, after the credits, the remains of KOS-MOS' body are seen drifting towards the planet. This is where the series comes to a closure.