"The fig in his hand was now the only thing he had in the world, that and the determination to see the great library of Sonnenberg." - To make this clearer, I would change the comma into a period and put a comma after "that."
"but none of the stubborn vines would yield its treasure." This should be "yield their treasures" because the word "vines" is plural.

"before the Cloud fell and the things he told me have haunted my being ever since" - I would place a comma after, "fell."
"It’s sense and intuition will be the key." - There shouldn't be an apostrophe in "Its."

"the worlds they’d encountered as if borne their own ideas" - I wasn't sure what this means. It doesn't make sense to me.
"He climbed up steep slopes, using shattered windows as handholds" - This is also not very clear. I think this is because it comes from nowhere. You haven't said the boy encountered buildings or anything that sounds like smashed buildings.
"lowers would settle down, growing in patches of simple rue, cerulean irises, and goldenrod tulips." - Rue doesn't feel like the right word here. I'm not sure it makes sense.
" offering a quite place of solitude" - A simple typo here. It should be "quiet."
I thought you could change the tense in which you write a lot of this story. You use : "would" and "had" words a lot. You could just write in the past tense, which some of this story is. But it would be nice to read this in a more definite tense.

"I tilted his bottle of beer and filled his glass." - This sentence doesn't make sense. No matter how I read it, I can't figure out what is actually happening here.
"a shaded snaking trail" - I would place a comma in between these two adjectives.
"A small raised fountain like for dipping a cup was in the center." - I would place a comma either side of "like for dipping a cup" for clarity.
"I can remember her words." - I would change "her" for "my colleague's", or something similar. You had just described the devil in the previous paragraph, so we need to know who "her" is in this instance.
I have a couple of comments on the use of speech marks. When a character is speaking over numerous continuous paragraphs, each new paragraph should begin with speech marks. Although, the only end-of-parapgraph speech marks come when they finish speaking. Also, more specifically, when you write, "Master, here is the man who yearns above all else for fame. "you need to enclose this in single speech marks because it is speech within speech.

"You don’t need to speak to be heard." - This sentence confused me. It took me a few reads to work out who was speaking. This sentence comes at the end of a paragraph which talks about the victim of the DeathBringer. But, I think it is actually Surranon speaking. Maybe move it down a paragraph for clarity.
"her still stiff frozen body" - I would add a comma between "stiff" and "frozen."
"Another thing the universe is wrong about us is ..." - This isn't clear. I would say, "Another thing the universe has wrong about us is"
"We were also created to learn too." - You don't need both "also" and "too" because they are saying the same thing.
"He continued sniffing while he started walking toward the entrance out of there." - I would take out "started." Without it, the sentence would be clearer and more definite. Just, "he walked to the entrance" would be great.
"I am one of them. we want ..." - Your new sentence, beginning "We want ..." should have a capital W.
"Waving his upturned hands at different parts of that room." - This sentence is incomplete. I would tag it on to the previous sentence by changing the period to a comma.
"I agree that Young Ones shouldn’t be victims, but I don’t about them know about us and what we do." - Did you miss out the word "care" after "know"?
My last piece of advice is to check your tenses. Throughout the story, you switch from past tense to present tense. For example, here: "He only takes a few steps before he stopped ..."

"Fighting amongst themselves to near extinction." - This is not a complete sentence. It reads as the first clause of a longer sentence. On its own, it doesn't make sense.
"12 manners of fruit monthly with leaves for the healing of the nation's." - The nation's what? This doesn't make sense.
"shelves’ full of books." - There shouldn't be an apostrophe in "shelves."
"They paused to study the text, this is what they read." - A couple of things. Firstly, the comma is incorrect. You could join these two clauses together by adding "and" before "this." Or you could replace the comma with a semicolon. At the end of the sentence, as you are listing what the petroglyphs said, you need a Colon after "read."
"One landed on top of Chris knocking him to the ground with fangs coming at his neck Chris sliced off its head." I would add two commas and a period in this sentence. One, a comma between "Chris" and "knocking." The second comma after "ground." Then, a period after "neck." Start a new sentence after that.
"A good night's rest and then early in the morning as Kat was preparing breakfast." - This is another incomplete sentence. What happened "as Kat was preparing breakfast."?
"The bird said 'that is quite a pleasant sound your wife is making.'" - To make this speech quotation correct, there should be a comma after "said" and a capital T in"That's."
"The boulders’ tare apart the raft." - Firstly, no apostrophe needed. Secondly, it should be "tear."

"Sophia retreated into her literary world, convinced that she would never marry and more in love with the literary characters ..." - This sentence is complicated. I had to read it a few times before I understood what you were saying. This could be fixed by placing a comma after the word "marry." Or, you could re-word it completely. Something like, "Sophia retreated into her literary world, convinced she would never marry. She fell further in love with the characters and worlds in her her books."
"The young man relaxed as if into his favorite subject and the light returned ..." - You need a comma after "subject" to make this read more smoothly.
You missed out the speech mark at the beginning of this sentence: "Yes, of course and especially if I get to read more.'" Also, there should be a comma after "course."
In the last few paragraphs, you have missed out the spaces between them a couple of times. Not a big deal, and easily fixed.

Damian says, "We have been here for Days!" - You don't need a capital D in "days."
"'Do something!' He cried." It should be a small h in "he."
"'Miss!' He said again." - It should be a small h in "he."

When you write "landborn" just check how you've written it because, once or twice, you write"land-born" and "land born" instead.
"'And easier to guess where your mind is.' Teased Jetta ..." - It should be, "... where your mind is,' teased Jetta."
Similarly, "'I would marry a land born before I would marry a Sunner.' Declared Jetta." - It should be a comma followed by a small letter.
"It seems like people are being sent to the Trench all the time anymore." - "Anymore" isn't the right word here. Unless you mean they are not being sent to the Trench all the time? If not, I would switch that word for something like, "these days."
" She did not want me to burden you with this much information before . before." - The period and extra spaces aren't quite right here. I would change it too something like, "before, before ..." A comma, then ellipses at the end would work well.

"... turned to Paul, leaning on his shovel watching, and said ..." - I would put a comma after "shovel" because it is Paul who is watching, not the shovel.