Each game in The Tale of Alltynex trilogy has an extra playable ship for the player to unlock. Note: Most of the ships can be used to play the standard story mode completely, but ZODIAC Ophiuchus can only be played through Area Select.

Ship	How to unlock
Advanced Armed Saboteur	Beat ALLTYNEX Second on Normal. Next time you select difficulty, the choice between standard and advanced craft will appear.
Mass-Production Model KAMUI	Beat KAMUI on each difficulty setting at least once. To use it, press right on the title screen.
ZODIAC Ophiuchus	Beat RefleX's story mode. The selection for your craft will appear only in Area select mode.