Read the chapters of 3Rei, as in, payng attention to the chapters, numbers and what's happening. The level of "meaning"/references just thrown in the most dumb way possible,
The very first chapter, Irya and Miyu being separated by light, Irya in a crater in a place that is cold, the city now a crater with the water farther than it should, her house now gone, with snow falling. The very first chapter could be said to literally represent the entirety of the arc, that literally repeats itself cyclically.
The characters, some are dolls, some install HS, some include cards, Gilgamesh Ko appears from no ******* where, HS literally transform in the middle of the process, Pandora, the box, has no ******* idea what is a person in the sense of the "Timeline" we are following, saying that it's either the Body or the Mind that is important, this same Pandora, as a box, becomes the foundation for Darius to become a giant with 3 pupils in each eye and arms in two directions that have a opposing layer in between, the giants that are generated by that are of "the species" that Darius becomes the King, while having their legs on water and their heads literally inverted, in the place of their torso/heart.
In the middle of it, Pandora lets the Mud enter one of the sides, and there's basically a mirroring of the scene happening the other side, but with diferent characters, while Kaleidostick talk and the "doll" Angelica asks who she's talking to. Shinji, donning the same Card as Illya, but instead of having the mask in the side, having it in the front, kills Sakura with a 3 petalled hole, that is equal to the corner spilling mud inside the other World.
I mean, you really ******* can't argue the story isn't about time and it's passage. And rephrasing the theme that man is the "doll" of Kami, while Kami are the dolls of Man. Kingu is Enkidu, the thing meant to anchor the Gods to Men is the thing that separates it, etc etc.
Literally everybody becomes a doll, merely controlled, a mind, the interplay of Body and Mind, and the origin of something as a Soul, hidden inside de Pandora Box that in the end isn't so hidden.
And to end it all, the very act of Darius becoming the Creator is him a puppet of his own tablets and crown of thorns, the so called King of Giants that he assumes control a puppet of himself, that can even notive that the "creatures" invading and his own sense of touch are the same thing, inverted, that dries and is just overthrown by Illya/Gil-ko/Tanaka.
And all Darius and Pandora can say is Pantha Rhei, everything flows, Pandora affirming "the Fire in his heart was gone", and therefore, the very process of life, of "output". He has 6 eyes but can't see a thing, cn't even differenciate Heaven from Earth, and said to have seen "a World where there were trees, evreyone was united" - the World where he himself is just headless "giants" that dry and die.
And them there's the reversion of meaning by Darius and basically everyone, everytime. Just for Darius to become dried mud - Earth, without nerves without heads or legs. And they will be them used as Earth Element, by someone else. Even the "incarnated Emiya Shirou" becomes oath bound, with his left arm covered, only seeing one way - the one Path. And probably this is the "Emiya Shirou" that becomes EMIYA, as he is the result of the Yumi and the Yari, the Crater that becames the Blade through his Blaze, while he is merely the receptor of the wishes of others.
And finally - Tanaka's Arm, shot - it becomes a Sword to be used through the Kaleidosticks, and is the Wings of a Dragon that cuts 90 degrees the attacks of others before (Yumi/Arc or Saber/Yari/Miya from will result in EMIYA A-3 letters-E, the family name of Emiya Shirou and the only meaning of EMIYA HS, because he lost all meaning he had)
From EMIYA side, as the HS that was thrown into a new World - Soul is definitely the same as Shirou's, but Mind and Body are really different. He won, actually, and now "He was always alone, intoxicated with victory in a hill of swords. Thus, his life has no meaning. That body was certainly made out of Sword." The body made of Sword is the Kansho and Bakuya held in the arm hidden, the arm is his life, he can only pray, as his hair, white, is the blade, always alone because the Shirou of before oathed and had only one path, trying to reconnect with the other side, his heart, the black sword, that became the torso clothing, the hair of previous Emiya becoming the Red shroud protecting him from the World. He was only EA, only air. It wasn't only Pandora that didn't understood "personhood", as she only new Mind, the thing coming out, and Body, the thing that is the touch.