The Valley of the Holy Spire is one of those places that a man could only dream of ever visiting, the place that I called home.
The comma should be a semicolon.
The rusted soil of the Mars gleamed under the light of the Faded One, the canyons nearby, made by the ancient rivers of fire, and finally, the most recent, but also the most holy among all of creation, the Holy Spire, the blessed creation, high unto heavens, ten kilometers tall.
This is a run-on sentence. I would suggest replacing the comma after "One" with a period and replacing "the canyons nearby, made by the ancient rivers of fire" with "the canyons nearby were made by the ancient rivers of fire." Get rid of "and finally" and instead replace the comma before it with a period. Say something along the lines of "The most recent feature, but also the most holy among all of creation, was the Holy Spire."
It’s dark skin absorbing all light, its glory still radiating everywhere.
Its, not it's.
Spiregarh, the small settlement of faithfuls, lived beneath the protection of the Holy Spire, which was the testament of our resilience.
"The faithful" not "faithfuls."
the head engineer, doctors, priests, and finally, Raj of Spiregarh stood at the front, being herald of the change
Get rid of finally. Is just Raj of Spiregarh the herald of change or are all of these people? If the latter, it should be "the heralds."
the corrupt corporates
This should probably be "the corrupt corporations."
However, the most holy imperative, which always was and always will be, is to find the Second Holy Spire, the one that shall cement our faith, the one that was never found in the Solar System itself but now hopes to be found in the nearest neighbour of the Faded One.
This sentence suggests that the spire itself is hoping to be found, not that the faithful are hoping to find it. Furthermore it goes on for too long—that's not grammatically incorrect, but it does make it difficult to read.
“Prepare yourself, oh faithful of the Spire and its Holy Saints, for the lottery shall be done tomorrow; twenty-five fortunate ones will be chosen to make the great journey through the void to find the sibling of the Holy Spire.” Announced the Raj of the settlement, leader of all of Faithful, stood at the podium, his hands made of sacred dark metal stretched furthest, body covered in Sikoi robes and face covered by the mask of black glass, two bright eyes of large size and a grin, digital in nature visible.
That period after "Spire" should be a comma and "announced" shouldn't be capitalized. You should replace the semicolon in the quote with a period. I would put a period after "the settlement" and instead say "The leader of all the faithful stood at the podium." "Stretched furthest" comes off as weird because I didn't think these people were all trying to stretch their hands. "A grin, digital in nature visible" should just be " a digital grin visible."
The ship drifted through space, the navigation AI charting the course for the next point in the deep void, like a fish swimming through the water, or at least what I watched in the videos.
Just get rid of the last comma and everything following it. Also, you have a change in tense in this section but aren't consistent with it.
“Are you interested?” I asked, sitting up on the bed. She looked curious, sitting up and checking my arm with the eye implant on her left eye.
"The implant on her left eye" will do; you don't need to repeat yourself.
She brushed her hand from my arm to my legs below my knees, also made from the holy metal, “Did it come from that alien thing?”
The comma after 'metal' should be a period. A comma would be appropriate if you had written something like "She brushed her hand from my arm to my legs below my knees, which were also made from the holy metal, asking." Furthermore I would suggest replacing "also made" with "which were also made."
“Yeah.” I answered.
A comma is appropriate here instead of a period.
“Ironic, a machine cultist is complaining about foreign objects.”
Semicolon rather than comma.
“Ironic, a machine cultist is complaining about foreign objects.” I smiled, using my normal left hand to caress her cheek, looking down at her body, wrapped around by a red dress.
Awkward wording. Just delete "around."
Her face was filled with an optic implant in her right eye
Her eye must be really big if the optic implant is filling it. I would suggest rewording this.
her left arm was a titanium arm
Just replace "a titanium arm" with "titanium;" you're repeating yourself.
part of her spine was also made from titanium.
How dose he know this?
“Don't worry, the Holy Spire is not some ancient weapon, and I will not turn into a monster or something.”
I'd suggest using contractions here rather than spelling out "is not" and "will not." The more formal cadence doesn't mesh with the casual conversation.
I said but she still looks unsatisfied with my answer. I smiled and wrapped myself around her.
Inconsistent tenses.
“So, we still have a few minutes till we reach; do you want some coffee?”
Generally people say "till we reach [whatever]," not "till we reach." Even if they don't name the place they'd still say "reach there" or "get there" or something rather than "reach," get," or whatever else.
I asked her, feeling her head nodding. I retreated, getting off the bed.
This is only grammatically correct if he feels her nodding at the same moment he asks. Also, it's an incomplete sentence. I would suggest instead:
“So, we still have a few minutes till we reach; do you want some coffee?” I asked her. I felt her nodding and retreated, getting off the bed.
I took my shirt off the floor, wearing it.
Should be "I took my shirt off the floor and put it on." Taking it off the floor isn't sufficient to allow him to wear it; you're skipping an action.
The water bubbled in the electric kettle, the two cups already on the table, filled with sugar powder, SynMilk powder, and some of ‘authentic’ Colombian coffee powder sprinkled on it.
This is a run-on sentence. I would suggest putting a period after kettle and rewording the rest of it.
You are missing a line break after "Thank you." It should be "came in" not "came." Also, is Catherine the woman from earlier? If so you should probably name her immediately rather than only in a different section, especially since they're narrated as going to the table together but she comes in alone.
We both sipped the coffee; it had the aroma, filling our nose.
What aroma? If it's a matter of it smelling like coffee it should say "the right aroma, filling our nose."
I didn’t know why; I
just liked her. She was gorgeous, like a star.
The line break after "I" shouldn't be there.
USMC Belisarius, once pride of an ancient superpower in 2100s, now stood at the Alpha Centauri system as the largest ship in the system, being 21 Km long and 4 Km wide, it was the largest ship of it’s time, travelling between Earth and Mars in every two year cycle.
Kilometers shouldn't be abbreviated outside of a technical document. The numbers should be spelled out. This is another run-on sentence; you should put a period after "wide." Travelling should be traveling. Belisarius should be italicized.
It is not known how this ship reached this star system, 4 light years away from the Faded One,
Again, the numbers should be spelled out.
but some believe that during the Crisis of the mid-22nd century,
Either crisis shouldn't be capitalized or Mid and Century should be.
once which used to hold goods
Which once used, not once which used.
“Heya home.” Catherine softly looked at the ship, the place where she was born, raised for a whole life.
Looked softly flows better than softly looked. Clearly she wasn't raised for her whole life there since by definition you can't be raised your whole life once you're an adult. I'd suggest just replacing everything after the comma with "her birth-place."
“Wire me 3000 dollars for this trip.”
Three thousand, not 3000.
this enough
That enough, not this enough.
“Done, we will meet next month.”
Replace the comma with either a period or a semicolon.
“Fine, I will find new spots till then for your hunt.” She waved at me before leaving the ship.
I'm not clear on what she's saying. Will she find new spots for his hunt or new spots until his hunt ends?
The cafeteria was the city square due to its unusually large size, and the command centre of the ship, once the brain of the entire structure, was just a glorified citadel of the elites, the ship having lost its ability to move anymore, bound to the gravity of the planet as its moon.
Run-on sentence. Put a period after "elites" and reword everything that follows.
The inhabitants, all machine cultists roamed around with their many augments, only exception being children below eight, being too small for such things but there was no mistake that these children were looking forward for one. I crawled towards Eddy’s diner, where we were supposed to meet.
If Eddy's diner is the name of the place it's "Eddy's Diner." "Being too small" should be "who were too small." "but there was no mistake that these children were looking forward for one" is awkward and I would suggest rewording. You're missing a line break following this paragraph.
The storage section C, an 800m wide cubical room,
Eight hundred, not 800 m, but exact dimensions feel unnecessary here since he'd be less likely to know them. Storage Section C should all be capitalized since it's a proper name and "the" isn't necessary in front of it.
Eddy’s diner was on the third floor of the monstrosity of the market, only a steel ladder allowing people to climb up.
"With only" not "only."
The diner was modest, filled with plastic furniture, three sides closed with the front side of the diner open to the rest of the market, the customers climbing in.
Run-on sentence. Put a period after furniture and reword everything that follows.
“Come on in; the fish will turn cold.” Gared, the old man said
Gared was not previously identified as an old man. Therefore it shouldn't be "Gared, the old man." It should be "Gared" and then later you can refer to him as an old man or show us that he is through description. There should be a comma after cold, not a period.
The other dug in while taking the fries instead.
Others, not other. Your wording also says that they both dug into the fish and took the fries instead; they can only have done one.
“So, I checked Vandalorum; the planet’s atmosphere is four percent carbon dioxide. No chance anyone can survive that place, even with floating cities.” Vivian told him he was tasked with scouting any habitable planet. “Our better bet can be Yamin-4, though its orbit is a bit wobbly.”
SPaG aside, 4% carbon dioxide isn't actually that bad. "Vivian told him he was tasked" is a run-on sentence. It should be
cities," Vivian told him. He was tasked with scouting any habitable planet.
“No sign of Holy Spire; others are still searching for it across the system, Rex, and some are even looking beyond the system’s boundary, though good luck scouting several light years.” Collins blurted out before putting a fistful of the arsenic-laden fish into his throat like the glutton he was.
Who's Rex? Also, isn't the main character scouting across several light years?
“Spire willing.” Vivian cheered by raising his piece of fried fish, others doing the same before resuming their eating.
"The others" not "others."
Belisarius entered the shadow of the planet, entering the nighttime of the nation, nestled inside it. The chatter of the hall got reduced to some mumbling of the guards the deck would send to maintain the order, the only other sounds being of micro asteroids smashing against the strong hull of the ship.
As worded, the station is nestled inside its own nighttime. Reword this. "Got reduced to some mumblings of the guards" is awkward; I would suggest replacing 'got' with 'was' and eliminating everything following guards. Put a period afterwards and say "were" instead of "being of." Also it's meteoroids not micro asteroids.
I slept inside a hotel room within the viewport of the ship, one of the few spaces down here, where outside space could be seen. It wasn’t your conventional hotel, though; there was no privacy, and everyone would sleep on the floor of the viewport, it being divided with curtains and sound blockers to give some semblance of privacy, allowing a total of twenty-four occupants, two in each room, to get a view outside. I was lucky to get a whole ‘room’ for myself.
This is just a hostel, which generally aren't referred to as hotels. Get rid of the second comma. Get rid of the scarequotes around 'room.'
I lay down, feeling a bit dizzy after drinking the local beer, made from once-used oil canisters. My metal arm is resting on my chest. The holy dark metal is still within my bones. It had been months since the search for the second holy spire had started, covering the entire star system, me combing the deepest voids with Catherine, and Spire willing, I was determined to find it.
The way this is worded, you're saying that the beer itself is made from once-used oil canisters. I think you mean the cans are once-used oil canisters. Also, you're changing tense again.
The lids of my eyes felt heavy, slowly closing while every organic part of my body was shutting down for sleep, Catherine’s image forming in my brain. A smile formed on my face.
Put a period after sleep and changing 'forming' to 'formed.'