Along with unlocking X's, Zero's, Axl's secret armor, the Navigators -- Alia, Layer, Palette -- can be unlocked as playable characters. If you completed the game on Normal or Hard and load the clear game file, the weapon for Navigator you used the most in your previous round becomes available in the R&D Lab. To unlock the other two Navigators' weapon, clear any four stages (can be done with previously cleared stages) with the Navigator you are trying to unlock. Alia, Layer, and Palette play as female counterparts of X, Zero, and Axl respectively, although Alia cannot use X's armor parts and Palette cannot transform into enemies. NOTE: Dispatching any of the Navigators will forbid you from having them help you in the stage.

Unlockable	How to unlock
Alia Buster	Use Alia as your Navigator often and clear the game, or clear any four stages with her in New Game+.
Layer Rapier	Use Layer as your Navigator often and clear the game, or clear any four stages with her in New Game+.
Palette Bullet	Use Palette often and clear the game, or clear any four stages with her in New Game+.