“However Ma always said that I was too kind so perhaps I was being optimistic about the Commodore’s looks. Also the bitch kidnapped my ship.”
Comma after “However”. Take out “that”. People tend to take shortcuts with their speech, so to make it real, taking an unnecessary word out here and there is recommended. Comma after “kind”. “Also” should have a comma after it, even though I’m not sure what you’re “also’ing”. The two sentences are at odds, so it doesn’t exactly make sense. “Even though” or “Still” would be better. Can you “kidnap” a ship? “Stole” would work better when referring to an inanimate object.
““I can see that,” Commodore Adel snapped before ordering me to move the ship, my ship, closer to the Way Station.”
Comma after “snapped”. Consider adding “excuse me,” before “my ship”, just to add a little dry humor. If not, just take out “the ship” entirely, in my opinion.
“It meant they were run by the military and had a limited amount of booze available.”
Consider adding “usually” after “It” to give the character a little more…character.
“Sure, I might be a slight five foot two woman but I can still out drink the largest of smugglers.”
Comma after “slight”.
“Helen Brooks was a name that sat in pride upon many neon boards boasting of my drinking prowess in Way Stations with proper names.”
Comma after “boards”.
“While Way Station Five might not have had a decent name it was certainly the most impressive station I had ever seen.”
Comma after “name”.
“It still possessed the eerie sense of hanging in nothingness that all debris in space seemed capable of, but it was only enhanced by the sheer size of the thing.”
The second “it” could refer to either the sense or the station itself. Consider revising to make that more clear.
“My eyes widened as it had stretched out before us, four times larger than the smuggler-preferred Branson, with its various windows and airlocks.”
You’ve switched from present tense to past tense with the “had”. Take that out.
““Right,” Commodore Adel said shutting down all of her transmissions and messages. “I’m getting no answer so we’ll dock manually.””
Comma after “answer”.
““Umm, do you think,” I began, giving the Commodore my best ‘are you completely fucking insane’ look.”
Rather looked like you began and ended the sentence right there. A better word would be “quipped”. In the event that you still wish to stay the course, use an actual interruption with a hyphen. It makes it seem more…interrupted.
“And of course con artists were even less respectable than smugglers so I was keen on letting them continue to believe their own tinted version of reality and hopefully get the command back of my ship.”
Commas before and after “of course”. Comma after “smugglers”. This seems a rather long sentence. Suggest breaking it up into two.
“I slowly eased the craft forward, the banged up old vessel swimming gracefully through the inky blackness of space.”
Comma after “up”.
“I’d won the old girl from a miner in a game of cards; well I don’t know if it’s called a game when you’ve magnetically charged the deck to your favour.”
Replace the semicolon with a period. Comma after “well”, in any case. And get that dirty “u” out of favor, you British bastard.
“After five years of gunfights, drunken piloting and a chase through an asteroid field the girl didn’t have much left.”
Comma after “piloting”, since it’s a list. Comma after “field”.
“And still the bitch singled her out at the mining plant that I was trying to con, demanding that I give them safe passage to the nearest military outpost.”
Recommend replacing “still” with “yet”. Comma after your choice, anyway. Add “had” after “bitch”. Replace “was” with “had been”.
“A lot of things had chance in the five hundred years since humanity first conquered the moon.”
“chance” should be “changed”. Recommend taking out “of things”.
“We hadn’t found any alien life yet but that was about our only disappointment.”
Comma before and after “yet”.
“And of course various private and national militaries guarded it all from scheming individuals such as me.”
Commas before and after “of course”. Replace “me” with “myself”.
“I spent most of my life alone within my ship floating through space, but the dental plan was excellent.”
Add “had” before “spent”. Comma after “ship”. “but the dental plan was excellent” seems out of place. Recommend taking that out, since you’re not really comparing it to anything else, as far as you’ve written. If you’re comparing it to the military or something else, say so.
““If they’re not responding how are you going to open the airlock?” I asked with a grimace as the ship grinded against the side of the Way Station in a shower of sparks.”
Comma after “responding”.
“Brushing the dirty blonde hair from my eyes I turned on the magnets with the flick of a switch, the ship clutching onto the side of the Way Station.”
Comma after “eyes”.
“Without even asking for permission the Commodore began to punch in a series of numbers upon the screen to her side, leaving grubby fingerprints all over it.”
Comma after “permission”. “upon” seems out of place, but that may be a British thing. Recommend replacing with “into”.
“Holding my tongue I killed the engine and waited as the ship shuddered to a stand still.”
Comma after “tongue”. “stand still” should be one word.
“A dozen different expletives soared into my mind at that moment; the only thing stalling me was trying to figure out the perfect combination for them.”
Add “the act of” after “stalling me was”.
“Instead I resorted to opening my mouth very quickly before clamping it shut once more, like a moron desperately struggling for air.”
Comma after “instead”. I liked the moron part.
““If you think I’m going to leave you onboard this ship while we’re in there you’re dumber than you look, Brooks,” the Commodore continued in my silence. “You’ll leave us there to rot and you wouldn’t give a damn.””
Comma after “there”. Replace “You’ll” with “You’d”. Take out “you”.
““Davis though smells a bit like mould and you actually look like it come to think of it.””
Commas before and after “though”. Comma after “it”.
“I wasn’t entirely sure what I was hoping for, perhaps the Commodore to throw a punch at me and then I could pull off the most daring Citizen’s Arrest in a lifetime.”
End the first sentence at “for”. Replace “and then” with “so”.
“Instead she merely ignored me, barking orders at the rest of her team, telling them to open the airlock and arm up.”
Comma after “instead”.
“Thanking her with a cheeky wink I slid the pair back into their respective holders, immediately feeling better about the whole situation.”
Comma after “wink”.
“I was slightly surprised when he too patted his hip to check that he had his weapon.”
Comma before and after “too”.
“You didn’t last long as a con artist if you didn’t trust you’re intuitions and mine were screaming at me that I would never see my girl again.”
“you’re” should be “your”.
““Just out of interest before I choke to death,” I said, gesturing at the walls around us. “Where are we going? It’s quite obvious this place is deserted, we should get going now.””
Either end the sentence at deserted and start the new one with “We should”, or replace the comma with “so”.
““We die perhaps,” I said as the doctor disguised his laugh as a hacking cough.”
That response doesn’t make any sense.
“Glancing to my left Susan was biting upon her bottom lip in steely resolve, it looked very cute.”
Comma after “left”, add “I saw” before “Susan”. End the sentence at “resolve”. Replace last part with “It looked rather cute.”
“Concentrate Helen, I said to myself sliding loose one of my pistols, this was no time for cute.”
Comma after “Concentrate”. Comma after “myself”. End sentence at “pistols”. Make last part into “This was no time for cute.”
“It did nothing to ease my sense of dread and by the time we reached the control room my heart felt heavy and my lungs sore, my limbs shaking at the slightest sound.”
Comma after “room”.
“It wasn’t fair, I didn’t want the truth, I just wanted to get the hell out of here.”
Make that into three different sentences. It’s okay for them to be short.
“Everyone always seems to be afraid of the sight of a corpse with the flesh rotting; perhaps a host of maggots eating away at what remains.”
End sentence at the Semi-colon. Add “it was the” after “perhaps”, taking out the “a”. Replace “remains” with “remained”.
“The Commodore swept into the room, one hand on a carbine the other holding the torch, before deeming that the area was secure.”
Add “and” after “carbine”. Suggest breaking off at “torch” and making the last part into “She looked around intently before deeming the area was secure.”
““Doctor, I want to know how long they have been dead,” she said, striding across the room without giving us a glance.”
Suggest replacing “they have” with “they’ve”. Like I said, people like to use shortcuts in speech.
“I wanted to look away or go after Susan who had positioned herself in the corridor but my legs had turned to lead, my neck stiffening with invisible concrete.”
Comma after “Susan”. “who” should be “whom”. Comma after “corridor”.
“Keanity began his work as gloved hands began to massage dying flesh and inspect stained bones.”
Take out the second “began”, as well as “to”. Replace “massage” with “massaged”. “inspect” with “inspected”
“I’m pretty good with the observational thing so my nerves didn’t calm as I saw his eyes widen twice either in surprise or fright in quick succession.”
Comma after “thing”. Replace “as” with “when”.
“Next time the military came to commandeer my ship I was running.”
Comma after “ship”.
“Either way would be preferable to the situation I was currently in.”
Replace “way” with “one”.
“In the Way Station though, the darkness and the mystery frayed at my nerves.”
Comma before “though”.
“My vision swam in that unfocussed way before I blinked in surprise and the thing skittered out into the light.”
The sentence reads confusingly. Maybe “My vision swam in that unfocussed way, the thing skittering out into the light as I blinked in surprise.”
“It was somewhere in between small and large, the same length and height as a coffee table.”
Take out “in”.
“Part of me was busying deciding whether it was a creature or a machine; the other half was deciding where the best place to shoot it would be.”
Make these two sentences at the semicolon.
“As it slumped to the floor, a part of its metal body pulled away to reveal a sickly green maw which cried out in pain.”
Since this is a bug and you’ve already said “body” in the previous sentence, I suggest replacing “body” with “chitin” or, since it’s metal, “chassis”.
“He ran his fingers across what I think was an arm bone before rushing over to the fallen creature, grunting that he needed a laser pen.”
“think” should be “thought”. Stop shifting tense
“Also they were capable of holding down a laser strike for more than two seconds without exploding in your face.”
“Also they were” should be turned into “They were also”.
“The doctor began to draw with the pen across the beast’s back, melting the metal as he went.”
Make this “The doctor began to draw across the beast’s back with the pencil, melting the metal as he went.”
“Sticking the pen within his mouth, Keanity pulled away the metal to reveal a mass of lumpy forest green flesh before the laser began drawing once more, this time revealing a skeleton as the meat began to drop from the bones.”
Comma after “lumpy”. Consider ending the first sentence at “more”. Add “it revealed” over “revealing”, if you choose to go my route.
““Fascinating,” the doctor murmured much to my surprise.”
Comma after “murmured”.
““No, see look it bleeds,” Keanity said pointing at where the Commodore had blown away the creature’s legs.”
Recommend replacing “see look it bleeds” *rolls eyes* with “looks like it bleeds”.
““It is nothing like I would have expected. It has an extra level of complexity than our bodies. A skeleton to protect the vital organs, flesh above the bones and apparently some sort of natural armour to protect the flesh.””
“It is” should be “it’s”, in reference to the shortcut thing again, unless this character has a habit of explaining things with no contractions, which is possible. Take out “than” and put in “compared to”. Comma after “bones”.
““Yes, those two bodies did display signs of being partially eating,” the doctor said without a hint of repulsion.”
“eating” should be “eaten”.
“As much as my mind screamed to retreat, I stayed with the people who had the really big guns.”
Feeling like I know the character, somewhat, it seems like she’d say “As much as my mind screamed at me to retreat, I figured staying with the people who had the really big guns was better for my life expectancy.” Just a suggestion.
“Without hesitation the doctor slid his hands into the thing’s mouth, feeling around for several seconds.”
Comma after “hesitation”.
“I tried to lock my eyes onto the doctor’s face instead but that quickly failed as he paled quicker than a drunkard facing a ‘full house’.”
Commas before and after “instead”. I liked that analogy.
“Suddenly finding oxygen to transport to my lungs became a far tougher job, my breathing shallow and rough. The thing that could reach up to my knees and probably charged me to the floor was a baby.”
Comma after “Suddenly”. Replace “charged” with “charge”.
“Commodore Adel had already rushed over to the control panel, opening up a layout of the Way Station on the big screen in front of us.”
Suggest replacing “had already rushed” with “was already rushing”.
“It was empty except for four dots in the middle of the map. I took several steps to the left and a second later one of the dots moved, the adrenaline coursing through my veins slowing slightly.”
Comma after “empty”, though it’s really more of a personal choice here, depending on how you’re trying to get this idea across. Commas before and after “a second later”. Recommend breaking the sentence off at “moved”, making the second part “The adrenaline coursing through my veins slowed slightly at the sight.”
“Then a blue dot appeared down a corridor on the far side of the station.”
Take out “then”. It’s not particularly needed, unless you want to keep it.
“It was one of those rare moments where time itself seemed to slow down as I watched tens perhaps hundreds of blue dots appear across the screen, most of them moving in one direction.”
Comma before and after “perhaps hundreds”.
“Most of them moving towards us.”
Personally, I’d use “Toward us.” Instead of that sentence. It’s informal and not a complete sentence, but telling the story in first person sort of lets that slide.
““They must have heard the youngling scream,” the doctor said and I couldn’t believe his calmness.”
Take out “and” and make this into two sentences.
““Commodore?” Susan asked and I saw her steadied the grip upon her rifle.”
“steadied” should be “steady”. Make it “her grip upon the rifle”.
“Strangely this felt better than the journey through darkened and dusty corridors, at least now I knew what we were fighting. Giant metal armoured spider aliens that could scream.”
Comma after “Strangely”. End sentence at “corridors” and make “at least…fighting” its own sentence. Comma after “Giant” and “metal”.
““There’s only one way into this room, you two keep control of that door for as long as possible.”
Break this into two sentences. Who are “you two”? Suggest using “X and Y, keep control of that door for as long as possible.”
“The assault rifle felt lighter than I expected, more balanced that I could have imagined, nevertheless it was a reassuring presence that calmed me.”
“that” should be “than”. Break off at “imagined” and make the last part “Nevertheless, it was a reassuring presence, calming me in such dire straits.”
““Look, I’m not willing to die for this, lets just get back to my ship,” I said, not turning my eyes away from the corridor and shadows in front of me.”
Break off at “this”. Make second part of dialogue ““Let’s just get back to my ship, okay?” I hissed, not turning my eyes…me.””
“And when they lost or broke that toy it hurts like a motherfucker, I’m sure they would say.”
Comma after “toy”. Turn “hurts” into “hurt”. Add an “as” before “I’m” if you really need to keep the last part in at all.
“My first possession beside the clothes off my back and my razor sharp wit was the now monster-infested ship.”
Comma after “possession”. “beside” should be “besides”. Comma after “wit”.
“I shielded my eyes from the highly focussed and bright laser that arched down the corridor and struck the alien, going right through its armour and roasting its internal organs.”
“focussed” should be “focused”. Take out the “and” and put in a comma.
“I hardly thought about it as I swung the gun around and pulled the trigger, the adrenaline taking control, as I peppered the beast with a volley.”
Take out the second comma.
“Holes appeared across its body, a liquid leaking from them, as it collapsed to the floor and I felt a surge of power course through me.”
Take out the second comma.
“They fell out from beneath it, the laser cutting them away, and the creature tumbled to the floor bringing down its companions.”
Comma after “floor”.
“I’d like to say that my aim was precise and thoughtful but by then the animal inside had seized me, taking control of the gun in my hands and using it to fulfil its most base desire.”
“fulfil” should be “fulfill”.
“Several seconds past before Mama Alien appeared, ripping her way in a frenzy passed the corpses that blocked her way.”
“past” should be “passed”. “passed” should be “past”. Wow, that’s kind of a coincidence. Hehe.
“Aiming for the underbelly of her armoured body I laid down a sustained burst of fire, Susan launching several powerful arcs at the alien’s head.”
Comma after “body”.
“Whispering a sincere word of apology I rushed backwards, planting a shot into Susan’s head, before leaping into the hole.”
Take out the second comma.
“Commodore Adel didn’t ask me where her solider was, she understood instantly from the look of disgust upon my face. Grabbing my arm in her harsh grip she threw me forward to where the doctor laid waiting in the ventilation shaft. He should be running I thought, the pain increasing as the Commodore’s nails dug into my arm and then I saw him up close. Keanity’s face was as white as a ghost, his muscles strained and visibly bulging beneath his skin. His left sleeve was rolled up to his elbow which was stained in purple blood that was spreading with every second I stared at it.”
Take out the first comma and make it a period. Capitalize the “she” after it. Comma after “grip”. “laid” should be “lay”. Comma after “running”. Take out “which was” and replace them with a comma.
““Must have dipped my arm into the puddle of the baby’s blood, probably a great defence mechanism that it’s poisonous to touch,” Keanity said, amazingly with a little grin upon his face. The doctor was insane; the good brave type of insane.”
Make the first comma a period. Capitalize “probably” after it. “defence” should be “defense”, unless that’s a British thing. “amazingly with a little grin upon his face” should be “a little grin on his face, despite how painful the poison looked.”. Comma after “good”.
“Before I could say goodbye though the Commodore was dragging me through the ventilation shaft once more.”
Commas before and after “though”.
“My legs were tired, my arms were sore and heavy and my eyes began to water in a salty concoction of grief and hurting.”
Comma after “sore”, since this is a list. “hurting” should be “hurt”.
“And my ship was loss to me. Somewhere down the shaft gunfire began to echo.”
“loss” should be “lost”. Comma after “shaft”.
““The scanner said there was no life forms, hot or cold blooded in here, I’m hoping it’s right.””
Break off at “here”. Make the last part a sentence on its own.
“I just wanted to leave the Way Station from hell.”
Say it like that, it sounds like she’s leaving the Way Station via hell. Instead of “the”, use “this”.
““And brought here when their transport needed new supplies before returning to Earth.”
Add “were” after “And”.
“Proof at last of life beyond our own planet. Except they outgrew their cages, killed the crew and to finish it off have an incredibly fast breeding time.”
Commas before and after “at last”. Comma after “crew” since this is a list. Comma after “and” and “off”.
At last, I am through with editing this tremendous bunch of errors. I, uh, mean. It was a good story. A little cliché, but nothing terribly cliché like my own attempt at sci-fi that you reviewed. Can’t really say I felt anything for the characters, though I felt like I knew Helen a little bit into the story. Not much emotion at all really. No real suspense. There wasn’t enough focus on how Helen felt. More dealing with her terror and initial fear would have worked wonders for the piece.
Dialogue was about your usual stuff.
I’m tired so I can’t really comment on anything else, so I’ll leave that to others who are better at critiquing stories, rather than errors. Though I will say this seems like your standard "Go in, find monsters, run away". I don't really see any future to it, but that might just be because this could be a perfectly good, self-contained story.
But thanks for your time anyway. 
