This was definitely an ambitious project—props for that.
I'm not necessarily 100% convinced that it all hangs together. The core of the relationship, between our two protagonists, is very solid, and it works well almost the entire way through. The rest of it, though, the Spear and the initial mystery and the odd meta-textuality, I'm not entirely sure of.
Initially, the bait-and-switch works: with the initial case, I thought I was just defining parts of the world as I would in any other game, but as the Spear revealed that it was actually it that allowed me that power, I was confused and alarmed. That moment really worked: it plays with the text-as-text and the fundamental interactivity there, and that's really clever.
After that, though... I'm not sure it all coheres. The fact that it takes such an arduous, specific explanation to cover Izanagi's power and Izanami's exceptionalism is rough. It shifts a fun-but-still-tense mystery drama to a heavy, weird fantastical story, and I felt myself getting lost. After the Spear explains the original myth I sort of understood it better, but the change comes so hard and so fast out of left field that I'm not sure it works.
I would recommend that you either drastically cut down the beginning mystery and focus entirely on the cave and the Spear, or else trim down the cave-and-Spear significantly, and have the mythological allegory stay firmly allegorical. As-is, your piece is caught between two extremes, and both suffer for it.
Still, there's a lot of potential here, and with some work I think it could be great.