i played it and was confused like everyone else. searching the web and seeing what others are saying, it's not so much a game as it is a short story told through in game format.
spoilers
the comments by 'a rob amongst many' and nocturnal kinda explain it:
http://www.rockpapershotgun.com/2009/05/19/deeper-gaming-fathom/
another comment:
http://gaygamer.net/2009/05/fathom_free_indie_flash_platfo.html#comment-146052
there's also other things nifty things like the green cpu on the start screen showing water = death. also there's probably some meaning to the fact that bad guys pretty much don't do anything unless you touch them (ex: the sprinklers cant hurt you, maybe the robot perceives them as bad guys even though they are harmless?).