A young lad just peeking into adulthood has lived his whole life in his hometown - the very large tip of a gargantuan stone tower almost entirely drowned in the middle of a vast ocean. 

Many centuries ago, a mighty calamity had engulfed their world and the only sanctuary left to his people was the mighty tower that loomed over their lands since ancient times. It is said that the blue waters that now filled their world chased thousands up the structure level by level and generation by generation until hundreds finally made it to the tip. To their surprise, a magically lush green garden in ruins waited for them at the top and by some miracle, the blue ceased its relentless pursuit and simply lapped at the entrance to their new home leaving them with a new lease on their world. Over time, the blue within the tower began to recede as if it were draining while the tides outside the structure remained the same as ever. It was thanks to this that the boy's people were able to salvage materials build anew and that he's able to dive downwards to pursue the lost mysteries left behind in their history as one the very few who cared to see beyond the blue. 

One day, fate makes it call as he falls into danger and a curiously carved stone falls into his hands. It seemed at first that he was to suffer the same drowning fate that welcomed unprepared divers of the past but that wasn't in store for him. Instead, he finds himself dry and the blue became non-existent all around him as he held the stone. It is on his ascent back to safety that he realizes the relic in his hands was somehow making it so that he could traverse the blue as if it were not there at all. 

The beginnings of adventure has him excited and he makes to show off his treasure but the surface was also seeing its own share of fate crashing down from the skies. A long extinct flying machine had been circling around their island for some time but something had gone wrong and it began descending quickly towards the town. Still managing to just steer the thing away from inbound harm, its pilots sets a course for the edge of the island where the boy stood long enough to see it miss its mark and get swallowed up into the ocean.

The boy stares in shock at what had just transpired but then he notices that a shadow was rising up from where the machine had sank. The pilot had made their escape in time but was now fighting for their life in the waves. The boy shows no hesitation as he leaves his equipment on shore and jumps in to help. He drags the pilot to safety and quickly gives aid to the unconscious victim in front of him but forgets himself when he strips away the soaking wet gear to find a beauty unlike any other girl he's known in his life hiding behind the oversized uniformed. He brings himself back into the moment and her back to the land of the living. Diver meets pilot and boy meets girl. This is the meeting that fate marks its prologue's end.

>Girl needs to get back to her back to her plane but there's no normal way to do so
>Boy has the way, climb down the tower, drain it level by level, get to the plane and use the stone to fly it out of the water
>Girl and the islanders have a very small common set of vocab so she has to take time to adjust before she can spill details but what she can tell them is that she came from an island in the sky to look for this tower
>First quarter of story is the prepwork needed to get the girl and the expedition team ready for the descent.
>2nd is a fairly comfy trek of puzzle solving and lore diving of the islander's history going up the tower and picking up more relics to make the tower traversable
>3rd kicks off with a reveal about the tower and its relation to the blue and many dark secrets the islanders kept out of their history from their descendants
>Last has them getting to the plane, fixing it up and has the pair take a long detour under the blue to see the ruins and scars of the past before they fly back up to the surface and to the girl's flying island after one more preptime montage
>They get to the girl's island and it turns out to be a colony ark that never made it out of the atmosphere and that the only people left were some families. The girl had actually stolen the plane to find one of the towers in place of her pilot grandpa who was too feeble to make the trips anymore. He slaps her for the foolishness but hugs her and expresses his thanks to the boy for bringing her back. The last pieces of the lost history fall in place as the girl shows him their records and it ends on them deciding together to bring her people to his island and begin a new search for the other towers.

The towers are the cause for the blue flood and the blue isn't real water but acts like it except for when tower magitech is involved. Way back when there were major wars going on using ancient lost magitech and some jackass triggered the towers' submerge protocol which were intended to shield the planet from the occasional cosmic storm but since the systems never detected the storm passing, it never went down the way it should have. There are actually underground shelters for such events but who knows how many of them actually served their purposes and if any still survive till now since they weren't built for long term use.

The airship didn't escape the atmosphere because of a damaged engine and navigation going whack but the power source was still fine and it's been drifting over the blue in circles the all this time. They've been fixing up and modifying the scouting ships for fishing and exploration but the ark only had so many food reserves and viable agriculture zones so population control was necessary. Dwindling resources, degrading tech, periodic failed resettlement missions and infrequency of fishing zones led to major depopulation over time.The tower on the other hand was built with stone on the outside so they served as giant coral formations where fish and vegetation would naturally get gravitate to and form a new ecosystem out of them.

When all is said and done, the main characters believe that they can find a way to deactivate the towers in the other ones and hopefully find more surviving colonies in the process hence why they decide to look for them at the end.