I've been thinking about the story and meaning of this game for a bit and here's what I've come up with so far:
In terms of the story, the hivemind has been subject to an experiment by the institution that tests the awareness of its consciousness. Like the game, this experiment exists in a continuous cycle: the boy will always come to break the hivemind out, the hivemind will always reach the same spot at the edge of the land in the light before the water (which was even modeled out, showing how it was planned), and then everything will be reset overtime; a new boy will be grown, the building will be repaired, and the hivemind will be restored, maintaining its thought from before (same with the player). The orbs are what reveal the existence of the cycle, since the ones you have previously shut off remain that way. This cycle can only be broken once the hivemind discovers the existence of the cycle and figures out how to unplug the boy, exerting the only true level of control it has in its world at all: the ability to stop playing the game set up by the institution. As a side not since this doesn't really fit anywhere into that, but I think those swimming things were failed versions of the boy who did not make it to the hivemind who have been lost control of and have gone rampant as a result.
In terms of meaning, I think it can be related to Plato's Allegory of the Cave in a way. The game is the cave for the hivemind, and going through the cycle is its attempt to break out of its cave - the world it inhabits - to achieve freedom. This freedom that the hivemind seeks is the water that lays beyond the light that it always ends up in; reaching the water is equivalent to exiting the cave. But, as both the player and the hivemind discover, they cannot reach the water no matter how many times they try. So the revelation that the player and the hivemind have is that the cave is a construct that they are subject to, that their whole effort to find freedom is just a part of the game and is controlled to the point where it can never be achieved, similar to how we can truly never escape the cave. By breaking the cycle, this signifies that we are exerting the only true freedom we have, which is to accept that the game exists and stop playing it. So pretty much the hivemind/player can only find the freedom they seek through truth.
Sorry if this didn't make much sense, it's late and I want to go to bed, but felt like I should try to explain what I think while it's fresh in my mind.
Well done.