@staika: Alright, I see. Still seems a bit out there but it isn't totally unthinkable.
Here, I'm bored. Let me try and spin something crazy.
Let's say that there was one charismatic guy who also happened to be totally insane. This guy believed that in order for the world to be in its most natural state, it would have to be fully covered in water. Let's also say that this man happened to be a college professor.
Over the years he spoke to bright but easily impressionable students and convinced them of his viewpoint, quietly recruiting them into his crusade and allowing his pupils to infiltrate various sectors of the world. His underlings find themselves seeded in a wide variety of fields ranging from politics to economics to science. As they work in their respective industries, they are quietly working towards the goals of their leader (funneling funding into his schemes, mitigating potential enemies, researching the technology to accomplish the flooding itself).
Finally, all the factors are in place. This guy is basically a supervillian with a doomsday device. However, there are no heroes to stop him. The crazy man with the crazy plan wins, flooding the earth and wiping out most of the world's population. Only a select few survive and adapt in their own ways. Some take to the remaining technology and adapt it to this new hostile world. Others begin to evolve to this new environment, taking on the fishy traits that you described earlier.
There, that's a far reaching conspiracy that revels in its own insanity. XP
[sub]I really should get some sleep, shouldn't I? o.o[/sub]