RPC Authority

The status of AEDF recovery operations for RPC-628 are ongoing, but the state being of RPC-628 is unknown.

Is this referring to RPC-628-A or the status of RPC-628 in the second half? May want to clarify.

RPC-628 was an aquatic mammalian organism measuring 430m long and weighing approximately 524,000kg that resembled a common Megaptera Novaeangliae(Humpback Whale).

Missing space between brackets and the scientific name.

While RPC-628 possessed a variety of anomalous abilities, the removal of RPC-628-A is believed to have neutralized the entity, and effectively caused the cessation of all anomalous properties of the entity.

Second comma can be removed. Can rewrite it, actually…

While RPC-628 possessed a variety of anomalous abilities, the removal of RPC-628-A is believed to have caused the cessation of all anomalous properties and/in addition to neutraliziation of the entity.

Footnote 14

Might end up getting back to this, ignore if I haven't deleted this.

Walking by the silent town

May be nitpicking, but a location name or descriptor of the town (gothic/Roman/ancient/relic/etc.) would help set the scene a bit more.

His clothes were far from clean, and torned in some parts, clearly this place was not close to home.

Separate into 2 sentences and fix the tense used for torn.

His clothes were far from clean, and torn in some parts. Clearly this place was not close to home.

His reasons for being at St. John's church were unknown, maybe to finish some business, maybe to start some more.

Assuming the church is named that way, you should properly capitalize (St. John's Church) to distinguish from the less famous St John's churches. Also you said before it was a Cathedral.

And so in the middle of the road the hooded man, walked through the common town.

Unnecessary comma. If you want to use them:

And so, in the middle of the road, the hooded man walked through the common town.

Though obscured, his hesitation to reveal his face was clear, the man on its surrounding nervously talked about him.

The clause used post-2nd comma doesn't really make sense. I'd delete it:

Though obscured, his hesitation to reveal his face was clear.

Add something else in there to describe his appearance more instead.

He answered with complete patience and with a calm tone in his voice, the stranger seems to know what's going to happen next, like an instinctive feeling.

You'd need to change this similarly. I'm guessing this might be to do with the conversation that occurs at the end of the paragraph.

Only one man had answered, opening the door slightly.

I'd say change the tense you've laid out to be wholly past, rather than switch between them. Let me know if you need a hand with that.

Only one man answered, opening the door slightly.

The man showed an annoyed expression, he questions their motives, the stranger, full of hope, replies with clarity:

Split into different sentences:

The man showed an annoyed expression. He questions their motives. The stranger, full of hope, replies with clarity:

And show, don't tell:

The priest's brow was furrowed, an expression of distrust etched into his waning face, as the door stopped suddenly. The visitor, oblivious to the man's state, stated with a speck of growing hope, "blah blah balh."

The young one was quickly silenced by the raising hand of the elder figure

I'm taking the young one is the visitor and the elder the priest at the door, hence use of the word waning earlier used, to signify an aged appearance. This should have also been described earlier in order to make identifying the two easier for the reader or changed to refer to their individiual professions/appearances.

who watched with judgmental eyes as the cloaked figure slowly pulled down his hood, revealing a wooden body, and a wooden mask, with wooden horns, that almost reached the sky from the elders perspective, and, of those horns, he broke each one in half and offered them as he bowed, handing the branches of his horns to the priest.

If you're using more than 2 or 3 commas in a sentence, stop it.

who watched with judgmental eyes as the cloaked figure slowly pulled down his hood, revealing a wooden body and mask with horns. The horns alone almost reached the sky from the elders perspective and, of those horns he broke each one in half and offered them as he bowed, handing the branches of his horns to the priest.

Also with the now-second sentence, I'd change the latter half:

who watched with judgmental eyes as the cloaked figure slowly pulled down his hood, revealing a wooden body and mask with horns. The horns alone almost reached the sky from the elders perspective and, of those horns he broke each one in half and offered them, bowing as the broken horns were placed into the elder priest's hands.

The motives for which I'm here for are not important, what is important is who is inside there, a long time friend of mine who is in need of help and I came here to do so.

Commas…

The motives for which I'm here for are not important, what is important is who is inside there: a long time friend of mine who is in need of help. I came here to do so.

The old man still with a doubting face slightly closed the door, as he was stopped by the wooden man who quickly put his hand on the door, to anyone else, that would have been four broken fingers, but to the wooden man? Only one. As he mumbled in pain he pleads once more, now looking directly into the man's eyes.

Commaaaaaaaaaaaaaaaaaaaas. Also phrasing should be changed. And tense…

The old man, still doubtful, began to close the door. As he tried however he was stopped by the visitor, quickly blocking with his oaken/birch/whatever hand on the door. To anyone else, that would have been four broken fingers, but to the young fellow? Only one. As he mumbled in pain he pled once more, now looking directly into the man's eyes.

Number's not needed, the sentence doesn't make sense in the latter half:

"I haven't seen Jonah in more than a decade. I can't remember his face anymore, but I do remember my name, so tell him that Ephraim is here."

This has no link whatsoever. Change it. Maybe…

"I haven't seen Jonah in more than a decade. He won't remember this face anymore, but he would remember my name - tell him that Ephraim is here."

The man had a slight discomfort to see that type of circumstance happening in front of him as if he had lived enough to know what is coming next. And even so, he closed his eyes, sighed one time, and said, as he closed the door.

I'm presuming this refers to the state of either Ephraim or Jonah. Clarify it in the prior sentence or this one.

After some time of the man waiting impatiently sitting on the stairs, looking at the stars of that cold night. And the sound of the door opening could be heard once again, the wooden man quickly raised to hear what the man had to talk about, once again, the door only opened slightly.

I'd change the sentence structure thusly:

After some time of the man waiting impatiently, sitting on the stairs and looking at the stars of that cold night, the sound of the door opening could be heard once again. The wooden man quickly raised to hear what the man had to talk about. Once again, the door only opened slightly.

As the group of priests starts to look from afar, the wooden humanoid starts moving towards the door, the man at the door raised a hand and said.

Set the scene - describe that there's a gaggle of priests watching this play out. They only show up now? Were they travelling with Ephraim? Were they outside the Cathedral/Church?

The group of priests had mixed reactions, some saddened, other, suspicious, for the man had walked for hours, sleepless to meet the one called Jonah on the church, and now he would finally be able to enter.

The group of priests had mixed reactions - some saddened, others suspicious. But the man had walked for many sleepless hours to meet the one called Jonah… and now he would finally be able to enter the church housing him.

The creature changed his clothes into a traditional monk uniform and started to follow the elderly man.

You've established his identity and form already. Why are you calling him a creature?

"He always did, Used N instead of M or E instead of A…

Change the comma to a full stop.

He stopped and looked past the mask and into the man’s eyes and Ephraim replied “I care not for the consequence of what I’m about to do…" Both fell silent for half a minute.

I'd change it to something like:

He stopped. The mask faced the elderly priest, the eyeholes boring into the saintly follower's eyes. “I care not for the consequence of what I’m about to do…" Ephraim finally admitted. The priest had no reply, his legs refusing to walk in disbelief/horror/whatever - it took a few moments before he lead on.

After that interaction, they went back to walking, to the deepest depths of the cave, where many mysteries awaited discovery. Soon enough, they reach a large portion of the cave where a giant whale lived. His name was Jonah Charte.

The hooded man didn't want his presence to be known, so his steps were silent as he slowly approached the whale in the pond. But once he reached the moss area, Jonah realized who was approaching.

to:

Finally they entered the target of the visitor - the cave of Jonah Charte, a water-sodden rocky, mossy crevasse. In the center laid the poor fellow himself - the aged whale and the defiled spear. Ephraim seemed to be coy in this moment - he found his footsteps falling quieter and quieter, trying to avoid disturbing his friend. But stir did Jonah, and in waking found himself face to face with a familiar face.

He smiled, when with it his mask did too.

Specify Ephraim here, otherwise it sounds like Jonah just grew a Deku Tree Mask.

"But I thought she hated"

Add a - at the end:

"But I thought she hated -"

""Exploring? She did… And also going outside, but since you left, she started realizing that those were the things you loved the most, and to come closer to you, she started practicing to become as big as her dad one day. Back in the day you were a big deal though… so when we heard the news, It was…"

I'd change punctuation a little here.

"Exploring? She did… and also going outside. But since you left she started realizing that those were the things you loved the most and to come closer to you, she started practicing to become as big as her dad one day. Back in the day you were a big deal though… so when we heard the news, it was…"

"Felt in love with humanity."

Regardless of implied context, fell's the right word here.

"Fell in love with humanity."

"What are you doing Ephraim!"

Can go a bit further here.

"What are you doing, Ephraim?" Jonah cried, then moaning as he felt the spear begin to budge ever so slightly.

The surrounding starts to shift and the air starts to become heavier as the presence of both entities start to clash severely as Ephraim's eyes dilated, he started to put roots around the harpoon and slowly pull it out, his hand starts to slowly get absorbed by the harpoon itself, Ephraim is quick to slash off his hand before it affects the rest of his body, and removes the Harpoon by infusing his vital energy to Jonah's body.

The surroundings start to shift - the air starts to become heavier as the presence of both entities start to clash severely. Ephraim's eyes dilated while roots encapsulated the harpoon and slowly pulled it out. His hand began sinking into the spear, inch by inch, but Ephraim was quick to slash it off without hesitation - before it affected the rest of his body. The Harpoon clattered upon the floor, finally free of the elder being.

It's literally the perfect home for someone like you Jonah."

Comma.

It's literally the perfect home for someone like you, Jonah."

"Eve blessed you with the ability to explore, she blessed me with abilities of healing, this is what I will do with this world, Jonah…"

"Eve blessed you with the ability to explore. She blessed me with abilities of healing. This is what I will do with this world, Jonah…"

Also, what is 'this' that Ephraim refers to? Uproot the Deep?

"I'm not feeling good Ephraim… My vision is getting blurry, my body is getting light, Ephraim, I ‘m… I’m scared…"

You've used multiple marks here, what.

"I'm not feeling good Ephraim… My vision is getting blurry, my body is getting light… Ephraim, I'm… I’m scared…"

Ephraim threw the harpoon to the wall

He cut off his hand, he's not holding onto it. Change.

"Tell them I'm sorry, I was a coward… Naive… and extremely stupid-…"

No need for the final ellipsis.

"Jonah stop saying that, for all that's glory stop, you have so much ahead of you."

Could use more exclamations.

"Jonah, stop saying that! For all that's glory, stop! You have so much ahead of you…!"

followed by Jonah's voice saying.

Jonah's speaking, not his voice. Choose 'Jonah's voice' or 'Jonah' and 'saying'.

followed by Jonah's voice. or followed by Jonah saying.

Ephraim comes up to Jonah and starts to lay his hand on him, a glow of green light starts coming up from his body and hands. He attempts to heal him in any way possible.

Get descriptive, man.

Ephriam rushes to Jonah's side again, laying his remaining hand upon his tought skin. Energy pours out from Ephraim and flows into the elder whale but if its purpose was fulfilled, one couldn't tell until they took a look at the poor wooden golem. The man was distraught, body wracked with fear, pushing more and more energy into his old friend as the glow enveloped them both.

"Things change, even if you want it or not Ephraim, those are my last moments, do you want to spend them fighting?"

"Things change, whether you want it or not. Ephraim, these are my last moments. Do you want to spend them fighting change?"

The whale starts looking up to the stars as he wondered what he is leaving behind, better, what he left behind, and with that in mind, he says:

The whale starts looking up to the stars as he wondered what he is leaving behind - better, what he left behind, and with that in mind, he says:

"Please don't say what I think you are about to say"

Missing a full stop there.

They sit in silence, both staring at each other for a few moments, as Ephraim comes back looking at the stars, before Jonah continues speaking.

They sat in silence, both staring at each other for a few moments before Ephraim returned to watching the stars, before Jonah continued speaking.

The roots start surrounding the whale, and they start rising from the floor, it wouldn't be needed though, Jonah would just float until he reaches there.

If you keep it, though I'd suggest something better:

The roots start surrounding the whale and they started to grow from the floor of the ocean. It wouldn't be needed though, as Jonah began to float until he was several metres in the sky.

"I hope you do, it makes me feel younger"

Fullstop.

A quietude comes as their eyes meet for one last time.

A quietude? A moment of quietude. That would read a bit better.

Ephraim bows as the roots start preparing, after a minute, a ground crushing sound is heard as the roots throw Jonah into the sky, in the direction of the sea.

Creativity

Ephraim bowed with respect as the roots finally acted. They curved toward the ground, almost like they were a ruler held to a table, before flinging forward and releasing the aquatic mammal skyward.

Also, wasn't he flying of his own volition? Clarify, man.

Ephraim starts walking back to the door of the cathedral, to his surprise, all the members were waiting for him outside, shocked to see him on the outside, they start asking questions

Ephraim began his trek back to the door of the cathedral - from the hole he had dug up, through the caves and back out of the cathedral again. To his surprise, the local clergymen were waiting for him outside, shocked after the events that they'd no doubt witnessed. ready to start asking questions:

On the way, he comes close to a forest, there he creates a wood structure, appearing to resemble a tree. The monks were shocked with such a performance, as they realized the tree had no leaves or fruits, only a stalk where he wrote a message with his remaining arm.

Describe how he creates the structure - does it grow up and out? Does he fashion it from the trees already there?