To briefly do a more 'traditional' review before I get to the stuff I actually want to talk about - at the end of the day, I think there's some flaws with the VN's presentation - the art style is consistent but hard to parse, the constantly pausing and shifting dialogue was sometimes hard to get through. This is specifically referring to the effect of characters pausing mid-sentence, not to the actual writing - the writing's really good, though the tone of the characters and their ways of speaking felt inconsistent from sentence to sentence which made it a bit rough at times. In general, I feel as though the presentation ultimately does the story here a disservice by making the VN a bit harder to get through than it should be - because I actually really really enjoyed the story here.
Now, in lieu of talking about the specifics... I just kinda want to share my interpretation of this story, because it's interesting and makes me want to talk about it and my interpretation of things (which might be wrong in places, but I feel as though it's better to share it than not to at risk of being wrong).
That said, I do want to give a warning and say that I think this story is best experienced blind, so to anyone reading this who hasn't played it, I'd recommend doing that first.
To me, Clam Story feels like a story about gods - both in the very literal sense of 'godhood' as an extradimensional being of a higher status messing with the world, and in the more metaphorical sense wherein one is in control of their own life and way of viewing the universe. Cheery has been toyed with endlessly by gods, has lost any and all sense of self, but within a world so devoid of everything - of culture, of people, of anything but the vastness of the ocean (which itself will soon disappear as the world 'ends' and Cheery dies) - they effectively become a god as well.
Much like how the god of leaves toyed with mortals endlessly in their pursuit of conquest, Cheery finds himself toying with Leeroy as well - in his endless pursuit of keeping the wolf from eating the clam, an act which will inevitably end the world by ending Cheery's own 'fantasy' of godhood. But... it's not as though said 'fantasy' is worthless - in the various loops that occur, we see a variety of possible ways in which things could shake out - Cheery could be crass, kind, to-the-point, omnicidal... and in viewing Cheery's shifting emotions, we get a glimpse into why the god of leaves might have acted the way they did - after all, what importance do the lives of mortals have to gods? What importance does Leeroy's life really hold to Cheery, when they will inevitably find themselves back on that beach after the world ends again?
Well, it's not like Cheery was all that happy when they were being an asshole to Leeroy, right? So why not be kind? Why not celebrate Leeroy's 'birthday', and make Cheery's own last few moments before death as kind as they could be by showering Leeroy with gifts and enjoying the little time Cheery has in spite of the pain of existing? In spite of their own failing bodies?
Or at least, that's the conclusion I came to from reading this. I do think there's also a lot to be said about Leeroy being a standin for humanity as a whole - a being so caught up in momentary pleasures and desires that they can't help but kill themselves due to eating the clam. That said, I've rambled enough already, so I'll leave it at that.
In conclusion, in spite of all I said - Clam Story did get me rambling a whole lot - and it made me give a spoiler warning so that people reading it will be encouraged to experience it for themselves, so... great stuff!