That line has never made sense. This isn't just a reactor? WHAT IS IT THEN? I suppose it might be the player's warning that there is a boss fight coming but by that point you can't do anything (and you probably don't understand how to do anything either) so it seems completely and utterly pointless.

Unless it was some sort of remnant memory of his time in Nibelheim Reactor. Because that really wasn't just a reactor.