In T.C. 4765 (Three years before the start of Episode 1), a space-time anomaly was produced as a result of the Zohar Emulators going out of control, when the U-TIC Organization was running connection experiments with the emulators at a facility located on the planet Ariadne. Ariadne completely disappeared within the anomaly, along with with it's 1.5 billion inhabitants. However, there were a few spaceships that had managed to escape. These included ships owned by the U-TIC organization. After the planet disappeared, it became a Gnosis-- the Cathedral Ship, which was a dungeon in Episode 1.
According to the database in Xenosaga Episode III (Also Sprach Zarathustra) a connection was made to the link experiment's director Andrew Cherenkov and the reason behind Ariadne being the location for the connection experiments. It was on Ariadne that Cherenkov was in a sham marriage, and committed murder repeatedly, and he had been placed in a personality reconditioning facility. This could be why he chose Ariadne to be the place for his martyrdom.