Xenosaga Freaks was only released in Japan and it contains 2 games, an Encyclopedia of terms used in Xenosaga Episode 1, and a demo for Xenosaga Episode 2.

The main game is XenoComi, an illustrated and voice acted text adventure. It has 6 scenarios to go through involving the main characters from Episode 1 and a 7th is unlocked when the other 6 have been played. It takes place at some point during Episode 1 and is much more light hearted. It focuses on the events caused by a rampaging cat-eared KOS-MOS and the event that led to the situation.

The other game is Kotoba no Puzzle: Xenopittan, a Xenosaga themed word puzzle game. Based off the game Kotoba no Puzzle: Mojipittan.