I read this VN because it kept getting posted here so it's Yea Forums The narrative is structured after Tractatus Logico-Philosophicus, a series of 7 self evident prepositions and annotations manifesting themselves into the 7 chapters of the VN.
Tractatus: 1 The world is all that is the case. 1.1 The world is the totality of facts, not of things. 1.11 The world is determined by the facts, and by their being all the facts. 1.12 For the totality of facts determines what is the case, and also whatever is not the case. 1.13 The facts in logical space are the world. 1.2 The world divides into facts. 1.21 Each item can be the case or not the case while everything else remains the same. 2 What is the case—a fact—is the existence of states of affairs. The beginning is a challenge to sum the facts of the unfolding prepositions, and so understand the world, beginning with Down the Rabbit Hole I. This seemingly serves as a prologue, and is the only chapter you cannot return to later, taken to be a dream of Minakami Yuki. The "true beginning" of the game, Down the Rabbit Hole II, starts with these prepositions: 5.632 The subject does not belong to the world: rather, it is a limit of the world. 6.41 The sense of the world must lie outside the world. In the world everything is as it is, and everything happens as it does happen: in it no value exists—and if it did exist, it would have no value. This the heart of the narrative. The subjects are each confined within their senses, we must piece together the truth of the Diskontinuierliches Dasein.
Each subject is their own world. This is presented to us in a roundabout way through the Kimika route of Looking Glass Insects, in which Mamiya Tomosane in his Yuuki Tomosane persona presents us with the idea of an infinitely large circle, created tangentially to a smaller circle. The infinite circle creates a perfectly straight line and encompasses all, reaching a state that might be called "God". This is representative of a deeper truth revealed in the final route, End Sky II. Each subject is actually within the sense of another, according to this principle.
>3.0321 Though a state of affairs that would contravene the laws of physics can be represented by us spatially, one that would contravene the laws of geometry cannot.
To visualise it, you might think of the purple circle to be Otonashi Ayana in her dream, the indigo to be Yuki in her dream, and the light blue to be Mamiya Tomosane and his associated personalities.
Ayana is the one figure throughout the narrative that doesn't fit into the facts left by the others until the final fact is in place. She is an otherworldly entity to the others, seemingly omnipresent. She constantly references outsideness to the world, and introduces herself as the daughter of Yog-Sothoth. Yog-Sothoth is the son of the central chaos Azathoth, and perched outside this universe he can see and manipulate all of space and time simultaneously. Mamiya Takuji thinks of himself this way in his madness... all within the outer world that is Ayana are like two dimensional ants crawling across a plane while she watches from above.
The final fact (End Sky II) is an annotation to the first fact (Down the Rabbit Hole). This fact is the Spirit Room and the Final Abode, which is the outer world of Ayana as seen by Yuki within the dream. The Final Abode is also seen by Yuki in a fraction of a second as she wakes, which is indicative of a second wakening as she almost emerges into Ayana.The Final Abode is a hospital bed.
The grand story of Minakami Yuki, heroic Mamiya Tomosane and his split personalities is only a dream of Ayana. What is outside Ayana? She provides an infinite multitude of explanations to Yuki. Is Ayana a figment of Yuki? Is Yuki a figment of Tomosane? Are they all a figment of Ayana? Yuki cannot explain it because she cannot obtain the facts or the true sense. The one thing that can be said from the perspective of Yuki is:
7 What we cannot speak about we must pass over in silence.