kazesenken
Honestly, it does lack the finesse, but I tried to make that scene more relatable(?). To describe the pain and what the MC is going through while he is in that realm.
And that's a better suggestion than what I had mind. I hope you don't me borrowing it when I edit the chapter later! (_')
Anyways, the first part of the second chapter was actually the important part of the content. In addition to that, the second and third part was to support it.
Here, let me break it down piece by piece, so that you can understand it better in my perspective when I wrote that chapter.
The scene of when the darkness started was with him being in the realm of the dead. That was with him still in a separate dimension that was in Eos, a realm that Etro, the goddess of death, lives in. She has absolute authority there and whatnot. She thinks of the Lucis Caelum family as her children, as would Bahamut, the astral god of light, does. So, whenever a member of that family dies, they would always have a place in her realm.
Exclusive right, I guess.
Now, when I described him being inside the darkness. He's doesn't know that he's in that realm. After all, while he does believe in astral gods, none of them really appeared before him to explain the situation, of what was going to happen to him next and why. He's in Valhalla. Well, the isolated part of the realm, but he doesn't know about it. All he knows is that he's dead and he's in a realm of complete darkness.
Imagine if you are in his shoes. You're dead, but you're conscious. You remember how you died, but you have no idea of where you are and how you got there. You believe in the gods and the stories that had passed on in your family, but none of them nor anyone appeared before you to at least explain the situation.
During those moments, all he has is own thoughts and assumptions. I wrote it in his perspective because I want my readers to relate to his experience, to see and feel what was happening to him during that scene.
Next, when the scene of him being submerged began, that was actually him being transferred to another realm, which was the Fate verse. Coincidentally though, the astral gods had dropped him off near to the center of the Akashic Records. I just improvise that scene because the episode in Kara no Kyoukai didn't exactly provided me a good glimpse of what the center of the Root looks like.
In the far off distance, it looks like a vortex Milky Way full of blue stars. The Type Moon wiki didn't help me either with my research, so I had no choice but to improvise in describing to the best of my ability. It's fine if it lacked finesse or such, because really, who can describe that place without the risk of being misunderstood even more by the readers that don't know much about the anime? Nonetheless, I tried my best and I have no regrets. I'm just bummed that the description of the scene turned out that way. Guess I'll just edit it later on...
After that, the scene with the pain and its various description is because of the connection to the Root is being made. Shiki Ryougi didn't experience because she was probably numb inside that realm. The MC was completely aware and felt those sensations as if he was alive and has a real body. By establishing a connection through the core of his soul, he felt that pain. The Root took an interest in him because he just appeared out of nowhere.
Hence, the result of the scene.
Next up is the scene with second part and third part of the chapter. It's actually spoilers, but I suppose it's alright if I tell you since it seems you're most curious about it. Well, on second thought it's not really that much of a spoiler since I just explained the first part. I suppose I'm at fault for writing the description too vaguely.
Anyways, the second and third part of the chapter was because Zelretch discovered that his own grandson has a direct connection to the Swirl of the Root. If Touko Aozaki was able to discover that Shiki Ryougi has a connection to the Root simply by observing the latter, then it would be easier and quicker for someone who had reached the Swirl of the Root to recognize the connection. Him being crazy happy and freaking out the Magi in the Clock Tower is the result of his unexpected discovery. That's pretty much it, really.
Also, Waver doesn't know. He only knows that Zelretch has a new heir to his legacy, but he doesn't know about the connection to the Root.
Hope this helps clear the vagueness of the chapter! :)