As might be expected, Keys are used to open locks. Keys typically only open one door; once that door has been accessed, the key has no further use.
Fred guards the Key needed to access Area 5.
A key is needed to access each boss chamber.
As in the original game, the Key needed to get to Area 5 is guarded in the depths of Area 4 by Ribbiroll. This key unlocks both a shortcut back to the top of Area 4 and the exit access to Area 5.
Additional Keys being necessary to access boss chambers is revisited towards the end of the game: Key 2 is guarded by Antibody Cell in Area 8, immediately due west of the shutter it unlocks on the path to the Mutant Lord. Keys 3, 4, and 5 are hidden throughout Area 9, required to open a triple shutter blocking off the game's final setpiece.