Thanks for all the positive feedback. I'll continue with this story, I know exactly where I want to take it, I'm just not so sure how to get there

Anyway, Here's the next update, a bit longer this time.
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Captain’s log, supplementalMy bad feelings came true; the away mission was a disaster, even though we achieved our primary goal. We managed to get the smuggler. But at high cost…Ensign Jones is dead…He was a good man, he worked in security…
He was killed by creatures that lived on the planet; they didn’t show up on our scans. They seemed to be fabricated…I think.
Ensign Trevok was badly injured, but the doctor says he’ll be fine, that sturdy Vulcan constitution of his saved him.
As for the smuggler…He was out cold when we got to him, but still alive. He is definitely humanoid, but not of any species I can recognize. Nevertheless the doctor hasn’t had much trouble treating him. I’ll include her report in the log.
He was certainly well armed and was able to take out quite a lot of those creatures…or machines, whatever they are. He used a sword that was an energy weapon at the same time, quite a powerful piece of technology too. I’ve told the engineering department to take a look at it, it may be useful. He also must have some sort of implant in his hands that can shoot energy balls…At least there was no outside sign of a weapon on or in his hands... The doctor said she’d look for it, though nothing showed up on her initial scans. But there must be something there…It’s not like it could have been done by magic or something…right?...No, of course not, there is no such thing as magic, only sufficiently advanced technology…Yes, well, anyway…[Pause]
All right, I’ve also sent an engineering and science team to the surface to take a look at these creatures; they are heavily backed up by security of course. I’ll interview the smuggler myself when he comes to. We still need to get into his ship.
[End of log entry]
Report of chief medical officer, concerning the alien humanoid.Computer, are you recording? Yes? All right…The alien is definitely humanoid, apparently male. He is 1 metre, 89 centimetres tall. Weight is 80 kilograms. He has a dark grey-black skincolor and bright red eyes. Other characteristics: long pointed ears, and what seem to be tattoos on his chest and hands. Standard layout of organs, or so it seems. Two lungs, heart in the right place…physiologically at least, right where you’d expect it for humans. Digestive tract seems to be that of an omnivore. Liver…also roughly where you’d expect it in a human…yes, just like every other major organ.
Iron based blood even…but his genetic makeup is definitely non-human.
The captain spoke of implants in his hands…no, there seem to be none of those present. Actually there seems to be nothing that could have caused the effects that the captain described to me.
A brain scan…now that’s odd, part of his brain seems to be much more developed, than you’d expect…computer, attach the technical details of the scans I made to my report.
The alien seems to have suffered from a blow to the head, by a blunt instrument most likely. There is a partially healed cut on his left side. Also…a broken collarbone, and an assortment of cuts and bruises.
These injuries are all treatable and will cause no permanent damage.
Ah, he seems to be waking up…Sickbay to bridge…
Recording of chief engineer’s investigation re alien’s sword. Also present chief science officer, ship’s anthropologist.CEO: All right, what are we looking at? A sword, heavy, about fifteen kilograms. A blade, total length fifty-two point three centimetres.
A: It seems to be a double-handed long sword, as is used by many species in the galaxy during earlier years of development.
CEO: Earlier years of development is all fine, but the captain told me what it did, so it’s got to be a pretty sophisticated piece of machinery…
And my tricorder doesn’t seem able to determine what it’s made of.
A: Don’t tell me the things are malfunctioning again.
CEO: What do you mean malfunctioning?
A: Well, you know after all that business at Meripala IV.
CEO: I told you that weren’t the tricorders. It was interference from their ore refining factories, and anyway this one isn’t malfunctioning, I checked it thoroughly.
A: Well…if you say so…
CSO: People, can we get back at the business at hand?
CEO: Yes, sir. So we know that it looks like a sword but we don’t know what it’s made of. It has to be technologically advanced, judging by what it can do. But I don’t see a way to get inside.
A: Looks like a sword, is used like a sword…maybe it’s just that.
CSO: Are you questioning what the captain saw, lieutenant?
A: Uh…no, sir…but maybe he made a mistake in the heat of battle, sir…That it was just a phaser blast deflecting from something.
CSO: So…you are questioning what the captain saw…You do know lieutenant, that phaser blasts don’t just deflect of something?
A: But maybe there was a deflector shield around something, come on…a sword that expels fireballs…give me a break…
Uh…but, er…that doesn’t mean that it can’t happen, sir…Uh, we have seen stranger things than that…sir.
CSO: Right you are lieutenant…Now, we have equipment to do a complete molecular scan. That should tell us what the sword is made of, and how to get a look at the machinery that drives it.
CEO: Um…Well, sir, if you say that we have the equipment…Well do you remember that ion storm we past through eight days ago? Now…It scrambled some of the diagnostic routines in our internal scanners…and, well…
CSO: Are you telling me that those scanners don’t work, lieutenant?
CEO: Yes, sir. That’s about it, we just discovered it just yesterday sir…But don’t you worry, sir, we’ll have it fixed in no time.
CSO: I’m counting on it, lieutenant, you can be sure of that
[Chief science officer leaves room]
A: Well, they’re not the tricorders, I’ll grant you that…
CEO: You, shut up…computer, end recording.