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In a world with no land, waves are actually not much of a problem. Waves are created by the water piling up against the land in most cases, or with waves merging into one another or being whipped up by storms, or any other number of things. Never the less, in a world with no land, massive waves are actually not that terrible of a thing usually, since all water movement would be only created by the movements of the lunar sphere ((or spheres as may be the case if Skytopia has multiple moons, which would go a long way towards explaining massive waves if such were the case))
But never the less, it is quite obvious that we DO have such a problem with aquatic habitation. Any ships we have are based upon sea planes, able to land in calmer waters between massive tides. The few water based platforms we have are built to be sturdy and stripped of all but the most essential functions, meant to be left to run and function without pause even when swamped by tides or waves, without any intelligent intervention. Even our largest ship, the great Fuseli, would not survive for long upon the open waves. Simply put, life upon the surface of the ocean is impossible for all but a few very intelligently designed vessels that allow the very waves to pass over them, built to be unable to be capsized, but even these are quite rare.
So what creates these massive waves that tear apart any normal vessels not built to survive them? The answer can only lie in the nature of the great upheaval itself, even centuries past, this event haunts us in ways far beyond the loss of land itself, it denies us almost any place to live except the skies.
Firstly, it is well known that the upheaval caused all land to either fall into the sea, or into the sky. But surely, the ground was firmly rooted and the sea contained within it like a vast bowl of salty water with a proliferation of life within it, how could all the land sink? The only answer is that the damage wrought by the original upheaval was far more grievous than any of us could originally imagine. I would posit that when the effects of the unobtanium weapons was finally felt, and the original skylands rose up into the air, they left deep cracks right into the crust of the planet, breaking the very continental plates that we know originally caused the disasters known as "volcanoes" and "earthquakes" that are spoken about in pre-upheaval events.
For the less well read skytopian scholar, or those just beginning their scientific exploration of the world, I will now explain what these earthquakes and volcanoes were in the manner described in a translation of the original texts about these natural disasters. An earthquake is very basically similar to how a skyland will shake violently under a great impact, or when parts of it fall off into the sea, or faults open up within it and the entire island falls apart. These would even occur on the ground apparently, with the entire earth shaking and rolling and pitching in the worst ways imaginable, even opening up vast crevices that could swallow entire towns in the very worst quakes. Thankfully, earthquakes of such magnitude were incredibly rare, and even regular earthquakes could only occur in specific places where vast plates of rock and earth met together on their journey over a grand ocean of molten rock and metals that makes up the core of the planet we live on. When two continental plates collided, or moved apart, it would slowly build up tremors and faults that would eventually give way and create earthquakes. These earthquakes even happen deep under the ocean today, creating the very largest waves that we know as Tsunami's, that can grow so tall as to sweep away low flying aircraft even!
Volcanoes are something even I find hard to believe, but if they do exist even today under the ocean, then they would go a long way towards explaining the terrible waves and violent currents we find on the ocean. According to the old texts, a volcano was a mountain, a vast pile or spire of rock and dirt upon the land, similar to the mountain we find upon Earthbreach. The difference lies in that THESE mountains were HALLOW! Instead, the very life blood of the earth, rock and metal so hot that it was liquid, much like the liquid ores we make in foundries but far less pure, and in such terrible amounts that when they bubbled up and out of the volcano they could sweep away miles upon miles of forests, towns, and lands under the terrible wave of molten metal and rock. These volcanoes often appeared in areas similar to where earthquakes happened, and earthquakes would often precede (or possibly trigger) volcanic eruptions. We can only be thankful that at the very least, the Upheaval relieved us of such land based terrors, and did not take them with us.
It could be theorized, that the Upheaval put deep and terrible cracks into the very continental plates, shattering them, and creating far more "edges" for earthquakes and volcanoes to occur at. These deep visures would be many many miles deep, deep enough, even, to swallow the majority, if not the entirety of the land that was not brought up into the sky, and this is exactly what must have occured. Those few lands that were not entirely swamped could only have been the very tallest of mountain peaks that were lucky enough to settle upon vast piles of other lands. Further, the only places under the seas that we can salvage from and even explore with the right equipment must have been from areas that were similarly lucky to not have been swallowed into these vast canyons that would have been created with the shattering of the continental plates.
What this means is that where once there were only a handful of fault-lines, as they were called, where continental plates met and drug against one another to create volcanoes and earthquakes, now there must be many hundreds, all grinding against one another and creating gaps down into the molten core of our planet, letting out vast amounts of heat and molten rock up into our oceans to create vast rising currents of water. Further, the many small earthquakes that must occur on a daily basis would create a great many "micro-tsunami's" as well as much larger ones along a few of the new fault lines. Combined, these two facts lead to great waves of terrible force even when, in fact, there is very little land left upon the world for waves to build up upon (these few being the very tallest mountain peaks from the pre-upheaval world).
But this alone wouldn't explain some of the erratic behavior of the waves and currents we see today. No, these can only be explained when one supposes that not EVERY unobtanium laden bit of land must have risen into the sky. Suppose, instead, many such bits of land that would normally have lifted high into the sky if they had been left to their own devices once loosed from the earth, instead were too slow rising. They would have been swamped by the incoming waves as the oceans poured across the former land. Once so swamped, they were too heavy, unable to break free from the waves. Other examples would have been far too weak to lift into the air, but perhaps not to weak to float about in the ocean itself, deep under the surface.
It is not too far fetched to believe that if lands can float freely in the sky, then there must also be examples of such behavior in the sea. Great masses of coral and ruin laden rock, with weak, unstable cores of unobtanium much like how our skylands once were without the stablizing elements of skystone, rocking back and forth, bobbing and moving in ways alien to the currents much as our own skylands do when they move against the winds around us. These great sublands, as I will call them, would displace massive amounts of water with their movements, much as a boat will displace water around it. As a subland moves, it would create a swell of water before itself in the direction it was moving, and a dip behind it, these sublands might even be the cause of massive sustained waves and tides and currents to be found in our erratic oceans.
Thus, when we combine sublands, with the vast undersea fault lines that must create a proliferation of deep-sea earth quakes and volcanoes is the direct cause for the erratic behavior of our planet's oceans, and from that, our inability to ply or permanently settle the waves in any fashion except aboard the most stable and well built of craft.
-Chapter taken from A Treatise on the Nature of Aquatic Habitation by Hetros S. Wukon