The story makes no sense?

Why did all the giants stop turning the crank? Never find out.
Why did the giants build a system that if they stop turning the crank they suffocate?
When did they stop turning the crank long enough to make the Omni Switch for Mo?
How did the fuses wind up on the opposite side of the room, and up on a platform?
Why do the giants turn to stone at the end?

These islands only have 5 inhabitants. They each live on a different island. Yet they treat Mo as the odd one for living alone.

In the end Mo doesn't have the Omni Switch. The Omni Switch was needed to power the machine that opens the door. Logically, once the door closes behind her she should be trapped in the cavern with Safan.

Bare with me, I only played (and finished) the game ONCE, and that was back in January of 2023.

Admittedly, I'd like to give the game a second playthrough during a subsequent Winter, but I'd have to be in a pretty lousy mood to feel like doing so; otherwise, too much else to play in the meanwhile.

Also, do pardon me if I sound overly harsh in any of my responses; I'm kind of just irritated in general, right now, haven't been getting enough sleep... For one who read well too much into the game's description, it sounds like you didn't read all that much into the game's actual plot... They were ALWAYS ALL DEAD to begin with, them being alive and working was a hallucination Mo was having, probably induced by the spores, and possibly also because of her own deluded hubris of wanting to be a hero that would save the islands.

We see scenes flash of one of the giants being dead (and underwater), and that's foreshadowing we see at multiple moments in the game, usually after completing major quests. Possibly an oversight on the part of the scriptwriters...honestly don't know how to explain this one, assuming you're not misinterpreting or misunderstanding something... Just common sense speculation, but that was probably one of the FIRST parts of the system they ever made: The key to control it. Don't remember what you're talking about here, but probably another oversight on the part of the scriptwriters. See my response to your first question: The big plot twist reveal is that they were always ALL dead. More like, they were all waiting IMPATIENTLY for Mo to discover for herself that it was best off to leave the islands; they were waiting for her to come to terms with reality. I think, if the giants were ALWAYS dead, the Omniswitch was ALSO always broken, and so was the rest of the system, so those doors were probably partially stuck open.

...

If I replayed this game, I'd probably either find plot holes like you have, or a newfound and better understanding of the game's plot, foreshadowing and symbolism.

Honestly, I'm just glad that ANY discussion is going on in these forums, because otherwise, they're kind of dead...

That's the 4th brother. On the last island you don't get to explore much of because it sank into the ocean. I could see his drowning and the failure of his machines putting a drain on the system as a whole but my other criticism is that the design of the system didn't make much sense. The story was a bit vague about the passage of time. I got the impression Mo explored the caves after the exodus, and the omniswitch was made for Mo. This is part of the puzzle design. For one of the fuses you have to push it off a high ledge to get it down to the slot it goes into. Assuming all fuses were in the slots to begin with there's no rationale for how it got to where you found it after being dislodged. At least the uncle cared enough about the purifiers to go stare at one once they failed. I don't think Mo had been imagining that they had been working all this time.