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Keep Circulating the Tapes: Coming out in 1999, you'll be lucky if you can even find a physical copy of the game anywhere on the net in this day and age. Thankfully Nyu Media rescued it in 2013 and you can find at DESURA, Rice Digital, GamersGate, or direct from Nyu Media for a very reasonable price.
Manual Misprint: In The Tale Of ALLTYNEX Guidebook, the KAMUI section indicates that the Mass-Produced ship fires at the same rate as the Alice ship. This is false; it actually fires faster.
There was going to be a stage between stages 5 and 6, using a Dark Reprise of "Final Hour", the stage 1 theme. It was scrapped, and the "Final Hour" arrange was instead used for the final stage of RefleX.
The final stage was going to have a scene where the Mechanized Temple crumbled to reveal the Final Boss, but time constraints resulted in the scene not being implemented.
Stage 5's boss would've had more bosses in its Boss Rush.