Abby makes a great point about hooking your reader!

I'll come critique this fully later on, but just wanted to point out one thing real quick:

“Were you headed?”

Shouldn't that have an h in it?   Automatic spell-checking devices are not to be trusted.

While I think that you have a unique premise and POV for this piece, I feel that the language used in this first portion was a bit too vague to really get a handle on. You do manage to communicate the saint's mystery and disgust with humanity, but other than that, there's not much to really grab onto in this introduction. I'll try to point out some of the parts that make me feel this way - but it's sort of hard: your writing's got a lovely fluidity to it, and I don't want to make the content too anvilicious - still, I think something's needed to make this really gripping.

The sound and tone of the very question: surprise and disbelief always caused a dull throbbing to occur at the back of his mind. It grew with every gesture they gave and every word they said after it. His body had adjusted to the situation and had already adapted an automatic reply.

I'm guessing that the question is: "where are you going?" but this isn't at all clear - not even after the old corn husker asks it. This, and the other passages like it also feel too vague - they use a lot of pronouns without antecedents. They also tend to be a bit repetative, telling us the same thing (raging inferno/pain in his mind/ hates humans) without adding much to building either the character or the conflict.

The reoccurring déjà vu caused an inferno in the back of his mind, exploding with such a violent motion his body would sink deeper into the numbing state.

first off here, a nitpick - you use the phrase "back of his mind" twice in rapid succession. Also, numbing state feels awkward when read. Why numbing state? Why not just "numbness" or "numb state"?

The realization had been a simple one and had always gnawed at the back of his mind, but had simply come to his vision only moments ago. He, like many others, had been ignorant, bathing within their pride of knowledge to ever realize the truth of humanity. Yet now, ignorant to the man next to him, the realization formed within his mind and hit him like the very Flood did to this land.

This, I don't get. The realization came to him only moments ago - so I'm assuming that means during the conversation with the old man? That's fine, if a little unclear. But You say that he "had been ignorant." But how is that different if he's "ignorant to the man next to him"? I'm having a hard time wrapping my mind around how this is supposed to be read.

it seemed that the mocking and irritated t one had flowed naturally from his lips.

bringing pain to the intelligent being

Aside from the typo in the top one, I like the idea of these lines - that there are multiple personas vying for prominence in the saint's head. However, I think that could be a more present theme, and really shine if you make it just a bit more obvious.

Basically, I think my problem with this piece is that the language is a bit convoluted, and tries too hard to hide the truth from the reader. I feel that this piece could be much stronger if it focused on making the reader feel and realize what the saint is feeling and realizing, instead of using veiled language. One thing that I think could be very effective is if you make the saint's realization the heart of this piece - don't just tell us what it is and that he came to it, but show us HOW he came to it and make us believe it too.

I do think you have an interesting premise, and I'm curious to see where it's going, I just don't want to be put off by language that hides the truth instead of revealing it.

I think Anne's critique is dead on.  The idea you set forth in the introductory description had me very intrigued, but unfortunately, we saw very little of that here.   I think Anne nailed it when she said you were intentionally trying to be vague in some places, which makes it both difficult to follow the plot, but also makes it hard to even really get into the story and care about the characters. 

I'm going to do a bit of a nitpick critique, because I think with a bit of rethinking some of these sections, you might be able to get the premise across in a more clear fashion.

It was always the plaguing question, the constant echo that seemed to roll off of everyone’s tongue.

Ok, words paint pictures.  I am wondering how an echo rolls off a tongue.  Also, this is an odd place to start.  I know you are going for a hook, but you might want to rethink having four paragraphs where you are in a sort of back story/head game with a character you haven’t introduced, with no action, no setting, just some discussion about

“the plaguing question”

that you don’t get to for four paragraphs, during which, nothing happens.

at the back of his mind.

This phrase is overused.  Some writers re-use phrases to establish a pattern or a catch phrase.  But here, it feels like you need to mix it up.  So, I’d suggest finding other ways to convey this idea the next few times it comes up. 

 Same goes for the words

Inferno

Realization

Ignorant

Simple/simply 

Unspoken

Liquefied

Here, I know it’s a typo, but what phrase do you mean? 

 “Were you headed?”

Honestly, I was so lost when I read this part, I had a very messed up visual of him asking

“were you headed,”

like, did you have a head in the past,  as opposed to now, where he’s been BEHEADED.  (Does that make sense?  I thought someone was asking him if he once had a head or if he never had a head.)

“So… it’s like some spiritual journey, or something? You going to face God, get approval, praise the Man?”

Who is “The Man?”  Is that what they’re calling God, or has someone set himself up as God?  I’d be more specific here if possible.  

This paragraph is confusing.  I don’t know who the “holy man” is, because if it’s the saint, you’ve got a POV hop issue.

The saint eyed him oddly, the look of annoyance mixed with pity flickered in his eyes and the man went back to shaving the corn. The holy man was going to talk, going to tell the man that his conclusion had been wrong and trying to drag the man out of the habit of humans, the realization which the saint had come to.

 “Golly… that seems like a lot,” the kernels of the corn fell into the bucket, the smooth metal moving in liquid movements. “I don’t think I’d be able to handle that, you’re a brave man.”

 Does anyone say Golly besides Goofy?  Also, the sentence about the bucket makes no sense.  Is the bucket moving in liquid movements?  The corn?  Later you reference a tool that he has, but it isn’t referenced here.  

Overall, the language used makes this piece very inaccessible.  It had no flow.  I re-read it to figure out that we have a man approaching the tower.  That’s a good opening—but it needs to come across that way. 

Also, after reading this twice, I still have no idea what the “realization” was, what the “inferno” was all about, and how that factors in to the question of him going to the city and the tower.

If you show your writing here, can you still submit to a publishing house later?  I like this but I'm very new in fact I joined tonight.  I am starting on a historic fiction now, chapter 1.  If I know I can safely show my start here, I'm going to do so for the community help.  This is really cool.

I'll do this as a freeform critique.  I liked flow of the piece.  It seems very much unfinished.  This made it difficult to grasp the storyline, however the writing flowed very well.  The question ...

Were you headed?

Was that supposed to be "where"?

Overall the structure and writing were very good.  I thought these two things a bit strange:

1. Inferno in his mind.  I might have used some other analogy.  I gathered this was droning or drumming and driving him crazy?

2. Liquefied his mind was a little weird.  Are you stuck with that?  It's okay, just an opinion.

Good job.  And, I hope that I helped in some small way.  I liked the story and want to read more.

David