After completing the game on Normal or Hard, load the clear game file. The weapon for Navigator you used the most frequently in the last playthrough will become 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:
HOW TO UNLOCK
Use Alia as your Navigator often and clear the game, or clear any four stages with her in New Game+.
Use Layer as your Navigator often and clear the game, or clear any four stages with her in New Game+.
Use Palette often and clear the game, or clear any four stages with her in New Game+.