Chapter XIII
Chapter XIII
"Come in," Captain Hazalk said as he tapped a few more buttons on his console.
"You wanted to speak with me captain?" Agent Ilisk asked as he entered the room.
"You mind telling me what Subject-38 really is? Or did you want me to lose another four soldiers before you admit your mistake?" Hazalk said in a perfectly level tone.
Ilisk shook his head at these words. "You failed to capture it? I am extremely disappointed in you captain, I was expecting-"
"When were you going to tell me that it was sapient? Or were you just hoping that I would look the other way as you attempted to sweep this whole thing under the rug?" Hazalk interrupted, his tone still completely level.
"...I don't know what you're talking about."
"Don't play coy with me, Ilisk. Subject-38 has shown the ability to use tools, has gained the support of the natives, and has shown a willingness to fight only as long as it takes to allow it to escape. It is clearly more than just a monster that the Krin Science Team grew in a tank. Unless, of course, it was designed to have sapience in the first place. If that's the case, then they broke an entirely different set of laws," Captain Hazalk said as he clasped both sets of hands in front of him.
"I never knew you were so squeamish, captain. I thought to expect more from the Hero of Thana," Ilisk said as he sat down in the chair across from Hazalk.
"Don't believe everything you read. In any case, I may have a stomach for war, but this is something else entirely. This breaks so many laws, that I don't even know where to start. My men also didn't know what they were getting themselves into, and that cost them their lives. Their blood lies squarely in your hands for not warning me beforehand," Hazalk said as he stared Agent Ilisk down.
"Don't give me any of your sanctimonious preaching. I have enough on you to get you the death sentence twelve times over, so if you're thinking of taking me down, I'll take you down with me," Ilisk said with a negligent wave of a hand.
If this statement worried Hazalk in the slightest, he didn't show it. In fact, Hazalk acted as if Ilisk had said nothing at all. "Not only did the Krin Science Team break the law, but by doing so, they have put our treaty with the Quzin Empire at risk, and need I remind you what happened the last time we went to war with them?" he asked as his eyes narrowed menacingly. "If they find out, the Krin will cease to exist, and it just so happens that this world sits within Quzin territory. I can understand wanting to put this under wraps, but in order to properly sanitize the crash site, I'm going to need to know what I'm dealing with. I'm willing to work with you here, even get in on your little operation, but first I need to know what's going on. So I'll ask you again, what is Subject-38?"
The two just sat there for what seemed like an eternity. Neither of them budging an inch, until finally, Agent Ilisk cracked a smile. "Captain, I didn't know you were such a risk taker. I take back what I said before about you being squeamish," Ilisk said as he leaned back into his chair. "Fine then, I'll let you in. Subject-38 and its fellows are the first experiment in a new type of warfare. They hail from a backwater, underdeveloped world, from which the science team abducted them and modified them to act as the perfect terror weapons. They were designed to be dropped on planets in large groups, to terrorize the planet so that when our boys showed up, they would be hailed as alien saviors instead of conquering invaders. Even when properly controlled with an MC unit, Subject-38 and its fellows would show an unbelievable level of intelligence and ingenuity, making them the perfect soldiers, and in turn, the perfect weapons."
"Were they ever tested?" Hazalk asked slowly.
"Yes, and to great effect. They brutally slaughtered anything that would get in their way, and showed great competence in group tactics as well as solo stealth missions. There was but one problem with the design, however," Ilisk said as he leaned forward.
"What was that?"
"Intelligence was what we strove for, it was what made the creature the ultimate weapon, and ultimately, that proved the science team's downfall. The team were going to test it on this very planet, but the weapons seemed to develop a... resistance... to our method of control. We aren't entirely sure what happened, but according to the last data packet we received, the entire stock had simultaneously broken free from their MC units and had proceeded to attempt a take over of the ship. We don't know what happened next, but I'm sure you can put together the pieces," Ilisk said pointedly
"Yes, yes I can. By the way, just how high up the chain of command does this little experiment go? I'll need to know who will be signing my checks for the foreseeable future," Captain Hazalk said pointedly.
"Magistrate Quazal, but no higher. I doubt the Hiarch or the chief of staff are even aware of the real purpose of our mission," Agent Ilisk said as he leaned back again.
"And that is all I needed to hear. Agent Ilisk, you are under arrest for war crimes and for being an accomplice to this entire affair," Captain Hazalk said as he rose from his chair.
"wha- captain, you're making a mistake. If I'm going down, you go down too. And believe me, your ledger is far more red than mine," Agent Ilisk said as he sprang to his feet.
"Don't make me laugh, Ilisk. The Hiarch is well aware of every detail of my past, and unlike you, I have his blessing. Didn't you get the memo?" Hazalk asked as he quirked his head to the side. Hazalk then strode towards a nearby cabinet and began to pour himself a drink.
He just barely raised the glass to his mandibles, however, when a burst of plasma fire struck him repeatedly from behind, throwing him into the liquor cabinet and smashing it to pieces. "I must have missed it," Ilisk said cockily as he stepped towards the smoking body in front of him.
However, as he raised his pistol to finish the job, the door behind him hissed open to reveal two armed Krin soldiers, their weapons at the ready. "Troopers, your just in time. Take this treacherous swine down to the brig. He was trying to-" Ilisk started to say, but was interrupted when one of the soldiers smacked him in the head with the butt of his weapon.
"The only traitor here... is you, Ilisk." Captain Hazalk said with a gasp. "Did you really think I would confront you without a contingency plan? The whole ship heard you confess AND shoot me. Take him away, and get medical up here as soon as possible, my vest failed when the scum shot me."
if only I had my camera... Hazalk thought as Private Vala grabbed Ilisk by the scruff of his collar. That look on his face is simply priceless...
* * *
Ow, my everything... I thought as my mind slowly became aware that it was awake. I tried to move, but my arms just didn't seem to be up to the task. Neither did my eyelids for that matter; but I knew I couldn't just fall back to sleep, not when my throat was as parched as Death Valley.
I attempted to stick out my tongue to lick my super dry lips, though my tongue didn't seem to want to work either. In fact, I was having trouble even opening my mouth, as strange as that might sound.
Speaking of sound, I found that I couldn't hear anything either. Well, that wasn't exactly true. I could hear things, but it was as if everything was muffled, almost as if I were wearing earplugs.
I seemed to be lying on something soft, with what felt like a pillow underneath my head. I wasn't too certain about that, though, because it felt as if my sense of touch was off as well. It kinda felt like my whole body had fallen asleep, everything being a close approximation of feeling rather then the actual thing.
There seemed to be someone in the room with me, though who they were wasn't something I could figure out at the moment. I tried to ask for help, but was foiled in my attempt as unconsciousness pulled me into its sweet embrace.
* * *
I became aware again when someone started messing with my bedspread. I wasn't really sure what they were doing, but whatever it was, it was keeping me from sleep. I tried opening my eyes again to see who it was, and instantly regretted it. Everything was just so bright that I had no choice but to close my eyes and groan in pain. “...why is the world on fire?” I asked in a raspy voice as I rubbed my eyes with a shaky, jerking hand.
Something about what just happened didn't sit right with me, but for some reason I couldn't understand what it was. Someone close by said something, but whatever they said was beyond my understanding. My ears still felt like there was cotton stuffed in them, however, so you could hardly blame me for that one.
“...can you help me? I seem to be having trouble with my everything...” I said as I rubbed my weak, shaking hand over the rest of my face. My hand froze, though, when it encountered a familiar, yet alien structure in the center of my face. It was small, round, and seemed to have two small holes on its underside.
Wait a second...
Slowly the clues started falling in place, but I refused to believe it. Was it all a dream? A nightmare? A coma from an accident? I thought as I tried to push myself into a sitting position. Someone nearby was shouting something, but my mind didn't even register the noise as my muscles strained against my weight. Ultimately, I gave up and flopped back down onto the downy softness underneath me, unable to even lift myself. What on earth happened? Was there a car crash? No, I was probably poisoned. That would explain the bizarre coma dream. Valerie probably rushed me to the hospital when she found me...
However, as I allowed myself to sink in further into the belief that I was home, a hoof touched my shoulder, instantly shattering the illusion that I had constructed for myself. How did I know it was a hoof, and not something else? Well, once you've been hugged by not just one, but two equines, the sensation is kind of hard to forget. Their hooves were hard, but covered in short, coarse hair. This created an odd, dissonant feeling whenever they touched my bare skin.
As interesting as all of that was, it was still beside the point. I was still on this weird, equine planet, light years away from home. As disappointing as that was, I couldn't bring myself to get worked up about it, or even care. I had awoken so many times in the past months in the exact same circumstance: believing a dream of home, only to have it torn from me by the cruel hands of reality. By this point it had almost become the norm.
There was something different about it this time. Not only did I have a nose again, but if my fingers could be believed, eyelashes, eyebrows and proper eyelids as well. The hair felt extremely fine, though, almost like a newborn baby's hair. As I moved my hand lower, I started crying when I discovered that not only were the fangs gone, but I also had lips again as well!
However, as I continued to explore my new face, something terrible began to happen. My arm, which up until this point had been dutifully following my every command, began to twitch and thrash, accidentally smacking whoever was nearby. Not to be outdone, my other arm began to join in, followed closely by my legs as they decided to get in on this action.
I tried to call out for help, but all I could manage was a strangled scream as pain shot through my entire brain. My pain was so great that I wasn't even aware of the hooves holding me down, or the needle that was inserted into my arm.
Unconsciousness claimed me soon afterwards.
* * *
I don't really know when I became aware of the voices in my room, but I had been listening to their strange, musical words for quite some time before I realized that I was awake again. I groggily opened my eyes, only to shut them again almost instantly. “...man, why is everything so bright...” I grumbled as I raise my hand to my face.
Or, at least, I tried to. Instead of obediently reaching my face and rubbing my aching eyes, my hand stopped as it jerked against the padded restraints holding me to the bed. This confused me at first, causing the more paranoid parts of my psyche to come to bear as I tugged against the restraints. The fear soon left, however, when a gentle hoof touched my shoulder, and a female voice hushed something nearby. Rational thought soon followed when I remembered what had happened earlier. They probably restrained me to keep me from hurting myself... I thought ruefully to myself. But why did I go into a fit in the first place? And where am I? Come on eyes, work. It's not like you're my most important sense or anything...
I tried to open my eyes again, only to shut them again in pain. “Why can't I open my eyes? Why is that such a chore?” I asked, not really expecting an answer. If the mare next to me gave one, it certainly wasn't in a language that I could understand.
Someone else came into the room at that moment, but seeing that I was effectively blind, I couldn't really tell who or what it was. They talked with whoever was nearby, the voice sounding male in my ears, then left in a hurry. “He's going to bring back someone to translate, right?” I asked. I knew she couldn't understand me, but that wasn't the reason why I had spoken. “You really don't appreciate the ability to speak until it's been stolen from you. Seriously, it has been six months, and the only voices I've heard have been the voices in my own head. And let me tell you right now, they are as boring as jelly-less, peanut butter sandwiches.”
On and on I went, but after what had seemed like an insane amount of inane banter, I eventually fell silent, letting my poor nurse have a rest from my bout of chattiness. After all, as fun as it was to talk at the mare in the room, there was only so much a guy could say before he became bored with a one-sided conversation. Besides, talking itself had become tiring, almost as if I had never used those particular muscles before. That makes sense, though. Whatever they did to me regrew the missing parts of my face. It only stands to reason that those new facial features act as if I have never used them before, simply because I haven't used them before, I thought as the door opened again.
Whoever had entered seemed to be female, judging purely by the quality of her voice. She sounded familiar to me somehow, though I wasn't really sure where I knew her from. This was surprising, seeing as how I was only familiar with eight of the natives, seven of which happened to be mares. This made the pool of people that she could possibly be very small, and I was certain that her voice didn't match any of them.
She said something to my nurse, and I heard her say something that sounded like an acknowledgement. She then left the room, closing the door softly behind her. My ears picked up the tale-tell hum of spell work, and soon afterwards, my throat and ears began to tingle. Must be doing what Star did... I thought to myself as the mare cleared her throat.
“Greetings, you having understanding towards me?” she asked uncertainly.
“Yeah, I understand. Mostly,” I said wryly.
“Good. Spell not perfect. Understanding not perfect. We teach later, say us tongue, yes?” she asked carefully.
“...yes?” I answered hesitantly. I couldn't be certain, but it sounded as if she wanted to teach me her language. I was okay with this, seeing as how our only method of communication was shaky at best, and a complete train wreck at worst.
“Good. Lessons happen later, happen questions now. We ask much, you ask much. Much learn, much grow. Yes?” She asked briskly.
“Okay... why does it hurt whenever I open my eyes?” I asked, fearful of what the answer would be.
She hesitated at first, taking a second to inhale deeply, almost as if she were steadying herself for something. “You... burn badly. Incredibly badly. Try heal, almost die. Use spell that... grow back lost. Two instructions follow, original follow, not... broken instructions. Spell nearly kill. Old instruction take over. Reject everything done. Reject eyes. Reject tongue. Reject teeth. Reject strength. Try grow new in old place,” she said apologetically.
I just sat there, my eyes closed as I listened to her explain what had happened through the broken translation. It was hard, but if I understood her correctly, then it sounded as if they had used some sort of weird healing spell to patch me up after the fight. It also sounded as if there had been complications, and that I had almost died as a result. But... did she mean what I thought she meant when she said that these 'instructions' rejected my body parts?
“What exactly are these 'instructions' that you're talking about, and what do you mean when you said that they 'rejected' my eyes, tongue, teeth and 'strength?'” I asked carefully.
“We know monsters take you, change you, give body new instructions. When spell cast, body revert old instructions. Nothing in instruction about claws. Eyes fake, been replaced. Teeth different instructions too, as tongue different instructions. Body think alien, is alien. Attack, kill, remove body, from body. Spell force body regrow new in place of old. Force us cut, remove fake devices before kill. Still attacking alien fakes,” she said apologetically.
Well, by the way she was describing what had happened, these 'instructions' sounded an awful lot like DNA. I wasn't a doctor by any stretch of the imagination, but I had watched enough Bill Nye as a kid to know a little about how genetic code worked. If she was saying what I thought she was saying, than it meant that whatever magic they worked on me had fixed the damage that the aliens had done to my DNA.
That correction had apparently come at a great cost, however. From the sound of it, my body had apparently then mistaken itself as a foreign entity, and had done its best to defend itself from itself. That would have been hilarious, had in not happened to me. Since it did happen to me, I nearly crapped myself in terror then and there.
“Well, its a good thing your magic was there to get me out of the woods, then,” I said in a fake jovial voice.
“Yes and no. Not done yet, body still attacking arms, legs. Try kill arms, legs. We slow, attempt fix, but may need remove and regrow. That we not want. Have re-learn everything, in bed for months, limbs regrow. Still could die. No, not done yet. Not safe,” she said ominously.
I just gulped at that as I tried desperately to hold onto my bladder. That right there was probably the scariest thing I had ever heard someone say. It certainly explained why I was strapped in, why I had gone into convulsions earlier, and why my arms and legs felt so weak and shaky. If my body was still busy attacking itself, then it was a miracle that I wasn't thrashing and howling in pain right now. Whatever they had me on must work though, because all I felt right now was a dull ache, as compared to the white hot agony that I had felt earlier.
However, as terrible as all of that was, it was paradise compared to the living nightmare that my life had been for the past six months. I could now look forward to a nice warm bed, three square meals, and a fresh supply of water. I didn't have to hunt for my food, and if I managed to get some money, I could get some clothes as well. Sure, there was the threat that my body would kill itself as it attempted to repair and regenerate, but that was just the chance of death. It wasn't certain, and I probably had a pretty good chance of surviving.
Out in the wild, though, death was a certainty. I had absolutely no illusions about my ability to survive the winter, despite my 'can do, will survive' attitude. I had only just barely made a pair of pants, and those hadn't exactly been the epitome of warmth.
On top of all that, I could now speak as well. Not just speak, either, but communicate. That alone was worth any risk. Honestly, I was still having trouble convincing myself that this wasn't some sort of dream.
However, as the minutes passed by in silence, it became increasingly obvious that it wasn't. This was the real deal.
“...Thank you...” I said as I softly began to cry.
She didn't say anything at first, almost as if she were shocked that I had shown gratitude for the pain and suffering that I was going through. “You're welcome,” she finally said.
We just sat there for a while as I tried to get my emotions under control. After what seemed like an eternity, I finally managed to get a hold of myself long enough to ask another question. “I don't believe I ever got your name.”
“Moon. What yours?” She asked in reply.
“My name's Alex,” I said, as the first smile I had made in months appeared on my face.
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I liked this. Good job author.
That being said, I am pretty curious as to where this story is going yo go next. I'm envisioning a first contact scenario coming up, and I love first contact scenarios. Well, second contact but you get the point.
Moona the Woona in June-a.
No wait.....
Awwwww yeah!
Super awesome chapter! Make very excited. Want read more story. Read now, read tomorrow. Much to take. Very happy.
Speak with captain. Captain be friend. Share rum with Armor. Make happy times war stories. Shining loose lunch or alien war.
Another excellent chapter!!!!!
I liked it...
I, LOVED IT!!
Yes, an excellent chapter indeed.
Cant wait for the next chapter!~
Aw, Luna is getting a friend. Also I'm happy that the Captain is smarter than the average alien. I'm just curious on what happens next.
you have proven yourself a worthy successor of the name science guy!
Another excellent chapter. Loving what you've done with the aliens too. Wonder how making amends will be like.
Well holy shit, the aliens aren't evil. That is certainly a surprise. I look forward to the future instalments.
I still love your story but I'm not sure how I feel about what seems to be a near full recovery. I'm all for happy endings but having him just suddenly switch to being fully human again feels somewhat cheap. I hope that if he survives there are some nasty side effects. Not that I would wish that on anyone, but it would feel less cheap.
Also very interested in the alien side story. I'm looking forward to a possible scene where they contact Alex and try to apologize for everything that has happened and explain their side of the story.
Why did Alex's name come out as 'Defender of People' before?
You should try to make the next chapter go over the same thing but from Luna's perspective.
so later, the aliens will make first contact and explain what happened?
5268760 Because it was going through the translator. This time the conversation was from his perspective, so everything he said was properly translated.
The same cannot be said about what Luna said.
5268753 It wasn't a full recovery. Even now his body is busy attacking itself, trying to tear him apart as it fights itself thinking that it is an invading organism. Not to mention that until his eyes adjust he is effectively blind.
5268693 Sorry about that. Already fixed! (boy, how did I miss that one?)
5268777 It does make sence that a comma would take place, try taking a plasma shot to the back, melting all your skin, muscle, and tissue off your body and keep conscious...
And my names Joy!!! Silly!!
The names Rage... and if you refered to ME as the depressed one...
No one is depressed here, I'm just the level-headed one. My name is Relaxation by the way.
It's good to see that it's not a cliche "evil" race. I find it hard to believe that an entire species can become sapient without developing a form of basic morality. Corruption and evil within a species is very easy to imagine however. Good job!
I love that the aliens are not just "oh we do this for the hell of it" and more of a realistic thing
The captain is AWESOME!
Oh no he's gonna be a bad guy
Yay he's REALLY AWESOME!
Shit he's dead
Yay he's alive.
Stop toying with my emotions like this! XD
5268906 It would help alot if you gave them more... understandable names... and forgiven.
Please ignore him, he lives up to his name.
You want another migraine?!?!!
I'll be... around...
In almost every HiE story I see, the human is either named "Alex" or "Anon". Would it kill people to at least be more inspired and come up with a lesser-used name? How about somethinh like Todd, or Chuck?
5268881
90% of HiE stories are cliché in some way, even if they're not intended to be. It’s just the nature of the beast, as it were.
5268889 No.
quickmeme.com/img/fa/fa2561b6ad4567d05eb1044912f1e734cf1766cbdd0f196484850a9ea8b2f81c.jpg
5268919 I actually wanted his name to translate to "defender of man" before I decided that his name was going to be Alex. I then fed the meaning of the name into google search, and Alexander was what I got.
Sorry for my unoriginality...
I assume he was talking to luna. I LOVED that beginning alien scene there. I like the idea that were are some actual good aliens out there. Maybe all is not lost now. I don't like the idea of a vast army of aliens coming in and wiping out equestria.
5268780 Well.. yes I get that. I'm just saying, even with the additional "recovery" chapter, simply switching him back to his human genome kind of undermines the "What I've Become" part of the story. I initially followed this fic because of the interesting premise of a human trying to survive in Equestria when he isn't human anymore.
Obviously, it has evolved since then. However, that is why I'm saying it feels cheap. It's like using the Elements of Harmony to make all your problems vanish in a big rainbow colored flash. I'll be following this regardless and I am looking forward to how it develops. Just my 2 cents.
5268927 Grr, and I'll love you for it anyway.
Because I am a fanfic masochist
5268943
It's not that its unoriginal, it's just probably horrible timing; you published the story when an influx of human named "Alex" stories (several by a very horrible yet extremely popular writer) were around.
I'm also jealous that you have a popular story, and I don't.
5268951 Okay, thanks for the constructive criticism. I honestly get too many comments like "MOAR" or "Cool.", but very little that I can use to grow and become a better author. So thanks a ton!
5268944
Nah, some rogue nation would launch inter-galactical ballistic missiles for that task.
5268961 You're welcome! If you want my opinion, I think it would be beneficial to his character to leave some kind of mark, or side effect, that he has to carry with him permanently. Maybe some kind of physical abnormality leftover from his mutation. Something that he has on him to remind him that "Yes, that did happen and no, you can't just forget about it and pretend like it didn't."
5268760
well, that and Alexander does mean Defender of the People and Alex is just the short version of that name, while keeping the meaning.
and he was speaking via a very very literal (the meaning of the word instead of the word) translator.
5269020 I did. His arms and legs are still the altered arms and legs that he got from the aliens. When the Krin Science Team took him, they removed his arms and legs and replaced the muscle and bone of those limbs with bio-mechanical substitutes. They then grafted on the modified limbs, leaving behind the skin and nervous system.
Oh my gosh thank you for not making all the aliens evil! That would have been bad. It is good to see they have morals and arnt one dime sinew bad guys. This story is awesome
I hope he gets Prototype-Esk powers.
Revenge is always sweeter when the enemy is hilariously out-gunned, and if he can grow claws at will and evade fire like he's gently swaying to a good song, I can tell Alex's revenge will be sweet as a lemon. 
You actually set up the bug aliens to be irredeemable monsters, then turned around and revealed to us that it was actually only a minority that knowingly committed acts that even their standards find heinous. You avertedand defied Always Chaotic Evil, even though you were in a position where you could have easily gotten away with it.
You have made my day, Author person (just in time, too). I am so in love with you right now that if you proposed, I would say y--well, no I probably wouldn't, but I would seriously consider it.
You, sir, have just made me promote this story from 'following' to 'favorite'
Love the chapter... but I'm also worried. You've got a story called "What I've Become" but now it seems like you're taking the "What I've Become" part out of it. This story has been different from and more interesting than the crap-ton of other HiE fics out there precisely because the main character has every appearance of being a hideous monster, and if you take that away I'm afraid it will become just another HiE.
5268925 yeah, i am mostly saying that it's NOT cliched for once, which is nice
5269098 5269020 The point of this chapter was I was trying to wrap things up. True, the 'What I've Become' part is over, which means that so is this particular arc. There will probably be maybe two, three more chapters after this one, but then this story will come to a close.
The sequel on the other hand... well, I don't want to spoil the surprise...
5269112 I've already guessed it. No point in keeping it a surprise. Obviously, the ponies were the bad guys all along. This is all a ruse.
I especially liked how you subverted the trope of the aliens being cartoonishly evil. This story might actually have...
Well, maybe not a happy ending, but certainly not a dark one.
5269112
It just seems like you had this great idea for a story but are bring things to a close without fully exploring it.
I like the idea its cool... and then he turned human... no no no no no no no NO! I wanted him to stay like he was ugh... ok not trying to be a dick man but uh... can I like say you should add a new alien or human amalgamation. Like uh fan made one.
5269210 That's what the sequel is for.
5268961
it seems that it serves you right 
Well if you are getting a lot of comments in style of a "MORE" and "cool" it just means you're doing something right
It's difficult to criticize when there's nothing to criticize
But if you want it I can still yell at you a little more
Maybe then we will see the promised chapter of Nautilus Protocol
Well, this was certainly an unexpected development - I figured that the aliens weren't going to be complete monsters given what the last chapter displayed, but it still came as a surprise as to how far the captain went to put a stop to the whole ordeal. Though thinking further upon it, I guess it's not that unusual - stereotypes about "evil aliens" aside, it makes sense a different society with developed individuality, so long as it isn't some sort of a hivemind, would have members with just as varied ethics, morals and view on life as we do.
I mean, I can certainly imagine there being humans who would be happy to experiment and try and weaponize alien life forms if they had the chance to ... and there being those who would be disgusted and affronted by the very idea of it, like the alien captain here. Pony society is already reasonably similar to ours (and has some bad seeds among it), why not another alien society as well, first impressions aside? Good subversion of expectations, indeed.
I wonder if we are going for a first contact scenario between Equestria and the aliens now ... I guess I can see it going both ways. On one hand, the captain seems straightforward enough that he would probably prefer coming clean and attempt to right whatever wrongs were done to Alex (possibly offer him a lift home?) - try and fix the whole ordeal as much as possible before these Krin catch wind of it.
On the other hand ... peaceful first contact doesn't really seem possible right now. From the captain's perspective, the natives would be aware of both the experiments done on the test subject, and their previous attempt to retrieve it (indicating they both want the test subject back, and their willingness to attack the natives to do so - since one of the soldiers opened fire on one of Luna's guards). With that in mind, he has no reason to expect anything but "shoot on sight" from the ponies where more of his kind to appear - and even if not, the chance to convince them this is anything but a trick to get the subject back when brute force failed is slim at best.
So he might be just as inclined to bug out before the Krin notice his ship's presence in their space, since he can't reasonably do anything for the test subject, and the natives seem to be helping him anyway.
---
The alien side aside, all the medical developments were highly interesting as well. And it does make sense that the ponies would be able to restore his original form (even if the battle for it is far from over, it was pretty good how his body was trying to fight and reject the changes due to the artificially attached limbs) - as we have seen in the show, they can perform transmutation of living beings with no ill side effects (Twilight turning a couple of mice in to full blown horses ... and her infamous potted-plant parents, of course), and even merge a living organism with a fruit ... that still somehow ended up alive (Twilight accidentally merging a bird with an orange ... and the resulting thing still flying away
) - so clearly they do have the tools to deal with an issue such as this.
And I'm looking towards the recovery period - watching Alex skuling around the woods was fun, but obviously it had to end at some point once he was found by the ponies and Twilight had established some form of communication with him (being the busybody she is, she probably would have done or arranged something eventually if aliens hadn't stirred things up first). This is just as good as any other alternative, and I'm looking towards it playing out. I wonder if Alex is due for a certain six visitors in near future ...
All in all, and excellent chapter and I'm looking towards the things to come.