I apologize for the length of this, I guess I got carried away. But that's what happen when you're interested.
I did this the easy way--for me and just included a few grammar suggestion in the text of your story instead of cutting and pasting, which can be more confusing. Anyway here goes, see what you think.
Deus ex machina V2
I knew MedTech Second Class Jonesey was potentially unstable. How he passed his PsychEvals and earned a berth on the UNSS Grackle, I'll never know.
I knew Jonesey was a homicidal lunatic — right from the moment the knife plunged into my back and punctured my spleen. The second thrust pierced my liver. Yeah. The man knew his anatomy.
I passed out — I died.
I watch Jonesey squat over my body; a low keening moan comes up from the depths of the god-forsaken hell that is his life — a coldly efficient psychopath he is not. I watch as he picks up my body — he is a big man, Jonesey — and carries it outside while the crew sleep fitfully (I had taken Grif's midnight watch; the crew were still in shock after Grif, N'guma, and Chauncey died exploring some of the ice caves near the ship.) I watch as he carries my body under the ship between the landing struts. I watch; moments later(,) as he emerges, sans body. I can't see what he does with the body — my body — but I figure he stuffs it in one of the exhaust tubes where it won't be easily found.
I'm a dead man. Not a dead man walking. No. I saw Jonesey take the lifeless body away. I. Am. Dead.
He returns to the ship, cleans up the blood — my blood — and disposes of the weapon. As I watch Jonesey crawl into his bunk and curl up for a peaceful night's rest, I have only one thought — my crew is in mortal danger(,) and I am a mere observer, a specter of my former self.
This started as an ordinary cruise of an ordinary survey scout ship with an ordinary assignment: find life-friendly planets for colonization.
But the crews of survey ships are anything but ordinary. And we were bored, tired of exploring planets in charted sectors of known space. Our Sailing Orders were deliberately vague, and crew morale and efficiency were suffering. I declared "Captain's Privilege(,)", ordered the nose of the ship to point to the Galactic Rim(,) and told N'guma, "Go." She grinned the same grin as everyone else — except for Jonesey. N'guma plotted the course, and (... this should be a dash —) we went.
Jonesey's eyes were wide with terror. I should have paid more attention.
I am in the ship's computer. Damned if I can explain it, but it is simple deductive logic. Fact: I am dead. Even Sherlock couldn't argue with that. Fact: I have motor and sensor control over ship systems. I spend hours experimenting with the lights and the airlocks. All my sensory info correlates to ship's systems: video, audio, tactile, olfactory, even my sense of taste is hooked into something — vile. I don't want to think about it, but when the ship's plumbing starts to go bad, I 'know' ...
Why couldn't my sense of taste have synced up with the galley?
When Jonesey had stuffed the body into the exhaust tubes, I couldn't see him because there is no external video down there.
The body. It doesn't even seem like mine anymore. The ship is my body; ship systems are my systems. I am the proverbial God in the Machine, but even I could not stop Jonesey in time. If I had figured that out sooner, I could have stopped Jonesey's murderous rampage; but they are all dead now.
Even poor Jonesey, crazed with guilt. We all get those terrors the first time out, past the safety tethers of civilization — alone, truly alone. I sat with him, unseen, just before he took his own life, listening to him. He died believing he was the hero, saving his shipmates from a fate worse than death. Jonesey had crewed before, but never this far out. My fault. And I feel nothing. I lost something in that transference.
There is something else here.
I am seeing, hearing, touching locations on this planet the ship's sensor array could never detect. I've hooked into something that doesn't belong here, something — alien.
No. Not a presence. An awareness. It takes time before I determine the awareness is a reflection — me, reflected in an alien architecture. A part of me is trapped there, as I am trapped in the ship's systems. I detect an intent within this (... this should be —) complex. Just as exploration and discovery are reflected in the ship's design, this alien complex has a purpose. It watches and waits.
The crew, the ship, the planet(—) ... it watched us. It watched and waited, until someone died. And then it trapped the essence of my death,(comma not needed here) before ashes became ashes, dust became dust. It(—) ... caught me; it caught my essence, before I could fade away, and entombed me in limbo. Purgatory.
(**)Purgatory, (a place) where imperfections are purified before ascending to heaven(this is a sentence fragment). And I know one more thing. My death — my capture — triggered an alert. Someone is coming.
I'm not sure I want to be purified. Dead or not, I'd rather stay here, on the planet I have named Limbo. I tried to take off, but the drive is down, its energies suppressed. That alien artifact has pinned me to this planet.
I can't find Grif, N'guma, nor Chauncey. They died before me, but there are many places I can't sense; maybe they died in the wrong place and couldn't be caught. And none of the dead since have been harvested. Unless we simply can't connect. This planet could be filled with the dead, and we would all be alone.
(** you might want to reword to something like this: Purgatory is a place where imperfections become purified before ascension into Heaven.**Heaven is the name of a place here and not "a heaven," and this example eliminates the passive voice.)
This planet is an anomaly; it shouldn't exist. It has nothing a space-faring race needs. It is barely habitable, (and) there are no industrial minerals. It is completely uninteresting.
The perfect trap. If you want to trap curious(,) and sentient beings, but don't want to attract scavengers, create a perfectly innocuous planet. And wait.
Because there is no such thing. Elegant perfection is the hallmark of mathematics. Everything else is corrupted by pockets of contradictions and chaos. Only the curious, the truly curious, will stop and ask — why?
Jonesey was right: we should never have come here. This is a planet-sized moth trap (A suggestion: This over-sized moth trap isn't a planet it's), a harvester, like craw-dad nets that let the craw-daddies in but can't find their way out.
But it's not trapping moths or craw-dads; this planet traps sentient life, life curious about the universe around them.
And the trappers are coming, (hell or some other expletive) they're on the way; I can feel it.
I don't know what they want, but I know I am about to find out. I am life — sentient life — dreadfully, fatefully curious about what hell awaits.
I wish they would hurry the hell up. Whatever is going bad in the ship's plumbing is becoming unbearable.
***Your story is superb. I like the idea of the ship's computer absorbing the main character's persona. Great idea. You move the story along in a rapid manner, nothing dragged on, and you chose your wording very appropriately for the narrator's characterization.
I found no faults in structure and only a few grammar issues, which I noted in the text. I made some wording suggestions, but they are only suggestions. I did notice one repeated point of contention (and I'm not really sure of that). It was (...) verses (—). In my learning of the language, the ellipse (...) is used for the omission of an implied word or words. The (—) is used to indicate a pause or stop in the sentence or flow of thought. Like you have in the second to last paragraph of the story shown above. I could be confused, so I would look that up before making any drastic changes, but that is how I remember it.
Your writing style is engaging and tends to make the read more "comfortable." And you certainly have the imagination of a writer with the talent to relay that imaginative tale to the reader. Keep writing because you have to.