• Published 3rd Jun 2012
  • 1,539 Views, 34 Comments

Proto-Element of Harmony - TheFanficStealer

Blacklight. In Equestria. This won't end well...

  • ...

Chapter 1: Glitch (Un-betaed)

Proto-Element of Harmony

By: The Fanfic Stealer

Disclaimer: I own neither MLP nor Prototype .

A/N: Figured I might as well update this before working on IASL Chapter 7. I’m sure some of you are curious as to how Mercer will handle his overall situation, and specifically his new body… his butter-yellow, pink-haired, absolutely adorable body.


Chapter 1: Glitch

Alex Mercer-- or rather, the sentient virus that took on the identity of Alex Mercer-- groaned as he slowly regained his senses. What the fuck happened? The last thing he remembered was… er… light? Yeah, light. A great, burning light from… er… from… from the nuke! That he’d been trying to get away from Manhattan! Now he remembered! After taking down that Supreme Hunter onboard the Reagan, he’d chained the nuke to a copter and flown it out to the ocean, where he’d dropped it and immediately tried to get the hell out of Dodge. Judging by the fact that his last memory was that of being vaporized, he’d apparently not been fast enough.

But-- and he actually found himself surprised at how utterly true the thought was-- he was fine with it. Elizabeth Greene was dead, the Supreme Hunter was dead, that asshole Randall was dead, Manhattan was saved, and-- most important of all-- Dana would be safe now. Just that last thought was enough to put him at ease with his current situation.

Speaking of which… so this was the afterlife, huh? Funny, he’d expected more fire and brimstone, considering the things he had done, not this… warm darkness… void… place. Sure, he’d saved Manhattan and Dana, and he was fairly certain killing all those Blackwatch fucks was more likely to earn him brownie points than marks against him-- considering Blackwatch mostly recruited their grunts from death row inmates, lifers, and dishonorably discharged soldiers with violent histories, they were a sick bunch, no two ways about it-- but… well, he was Blacklight, a sentient virus that essentially ate sentient beings and stole their experiences. He was also Doc-- err, the legacy of Dr. Alexander Mercer, a psychopath that had willingly taken an entire city down with him in death. He was fairly certain just those last two would be enough to have him Hell-bound, and that wasn’t even including the thousands of innocents he had killed and/or consumed in his quest to… well, he’d had a lot of goals, so let’s just call what he did his “quest” and leave it at that.

Not that he was complaining, of course-- unexpected or not, he was quite glad he wasn’t burning in Hell, thank you very much! Seriously: warm, comfortable void? So much better than pain and agony for all of eternity. Sure, he’d probably grow bored of having nothing to do but float around and be comfortable before long, but he would cross that bridge when he got there.

…Huh. That’s… strange. Did he just feel a… tingle? Why was he feeling… tingly? And not the good kind of tingly, either-- this was that really annoying tingly one got from moving a limb that’d fallen asleep… something that was impossible for him, by the way, technically being an amorphous blob of biomatter and all. And physically impossible sensations aside, he was fairly certain he shouldn’t be feeling anything, since he was now merely a consciousness floating in the darkness… or was he?

Actually, now that he thought about it… this “darkness” seemed awfully familiar. In fact, he was receiving signals that pointed at a rather embarrassing fact: instead of being in limbo and having an epic monologue espousing on how he had no regrets dying a hero, as all tragic heroes were wont to do, he’d apparently just been mentally bitching and moaning in semi-unconsciousness.

Well… damn. Now he felt like an idiot.

In an attempt to forget his humiliation as quickly as possible, he decided to instead see where he was. He slowly opened his eyes, wary of being blinded by possible bright light. When his eyes didn’t immediately and involuntarily slam shut in burning, mind-numbing pain, he opened them the rest of the way and took in his surroundings.

At first glance, it seemed like maybe he really was in hell: the ground was covered in ash, there were several fires around him lighting up the surrounding darkness, and the air smelled of smoke and soot. But a another look revealed that, despite his immediate surroundings, he was merely in a forest clearing-- while the area for a short distance around him was desolate, beyond that stood trees that, even in the gloom of night, he could tell were very much alive, if not slightly charred. He breathed an internal sigh of relief for not being in a hostile environment, and finally attempted to stand up… only to fall on his back as soon as he was upright, discovering at the last minute that something was very, very wrong with his body’s center of gravity.

“…The fuck?” he muttered out loud, trying to figure out what the problem was… before realizing that the voice he’d just used was most definitely NOT his. It was too soft, too light, too… feminine. Was he in the form of a little girl, or something? He shouldn’t be, considering he was fairly certain he’d never consumed any children… at least, he had no memory of doing such, and he didn’t have any foreign memories from children.

He rolled over with the intention of trying to stand up again, only to be met with pain half-way through his roll. He still completed it, but it had hurt like a motherfucker—much like getting kicked in the nuts, if he had to find an analogy.

Back on his stomach, he once again tried to stand up, making sure to be careful this time around. He slowly got on his hands and knees, looked down to see if he could catch what was causing him to fall down… and promptly did a double take at the sight that greeted him: where there should have been hands were now yellow hooves, and where there should have been arms were furred forelegs of the same shade as those previously mentioned hooves.

“The FUCK?!” he cursed, twisting his head to study the rest of his body… which, instead of the gray and black and—most importantly-- humanoid shape he was familiar with, now resembled that of a pony—too small to be a horse, he absently noted—with a uniformly yellow coat, a pink tail, and… were those fucking WINGS?! Holy shit, those were wings! He was a fucking pegasus pony mutant thing! That could talk! How--? Wha--? Huh?!? He-it-how in the FUCK?!?

…Huh. So this is what having one’s brains dribble out of one’s ears feels like.

It was several moments before his brain stopped melting and somewhat recovered… and by “somewhat recovered” he meant “sacrificed a bit of his non-existent soul to the god of insanity, specifically the part that imitated Alex Mercer’s inner scientist.” He hadn’t figured out how he was a talking pegasus pony mare (and he was most definitely a female— if his new voice hadn’t given it away, his lack of certain body parts certainly did), but that could wait until later, when he wasn’t in a burned out clearing and his mind wasn’t threatening to collapse in on itself.

And so with that thought, Alex started making his way out of the clearing, no clear destination in mind other than “outside the forest” and “somewhere safe.”


A short while later, Alex found himself standing before a homey-looking cottage situated on the outskirts of the forest. It was a two storied building with a roof that seemed to be thatched with green foliage, partially surrounding by a babbling brook that was crossed by a small bridge. It was rather idyllic, almost like it had been ripped straight out of a children’s storybook. And while it wasn’t quite Alex’s cup of tea, he had to admit that the serene nature of the cottage had a certain appeal.

Unfortunately, that had to take a backseat to something Alex noticed during his short walk: he had no new memories. What’s more, despite the lack of memories, he had the strangest feeling of familiarity as he approached it, as if he had known where he was going. The cottage itself, though quaint and serene, gave off a feeling of safety beyond that of an ideal living space, almost like he was looking upon a refuge, a…

“…Home…” he whispered before he knew it, realizing that this must have been where the pegasus (that was what he was going to call them until he either came up with a better name, or found out what the locals called themselves) had lived. With this epiphany came the realization that the memories were there, but, for some reason, he couldn’t access them. That worried him, as it raised several questions:

First: what was keeping him from his current form’s memories? To his knowledge, nothing was capable of doing that-- the bout of “amnesia” he had when he consumed the original Alex Mercer was the closest thing he could think of, and that was merely him assimilating his first set of memories. The memories of all those that came after had been easily accessible to him after the initial info dumps, from regular humans, to infected, to hunters, to D-codes. Even Elizabeth Greene’s memories were accessible, and if there was something that could interfere with a complete assimilation, it would have been Redlight!

But back on topic: something about the pegasus he’d consumed was actively blocking his access to her memories. Was it biological, a featured shared by all of her kind (assuming, of course, she hadn’t been unique, a laboratory experiment that had been given some leeway)? Genetic, something only she or someone related could achieve? Whatever it was, he needed to fix it soon, as the lack of memories led to…

Second: what was he going to do now? With no memories to rely upon his options had become severely limited:

His preferred option, going incognito, was no longer available, as he could neither integrate himself into whatever society was nearby by taking the pegasus’ place, or literally hide himself away, lest he raise the suspicion of those that had personally known the pegasus.

There was also no way in hell he could just explain his situation, as any explanation he could give would basically boil down to: “Hi, I’m a sentient virus that survives by consuming organic beings of all shapes and sizes, and I regret to inform you that your friend/lover/pet(?) was accidentally put on the menu last night. Can we still be friends?” Yeah, right. That’ll go over real well.

And, finally, he didn’t know enough about the local military for violence to be an answer-- if they had access to whatever was keeping him from fully assimilating the pegasus and modified it into a weapon to use against him, fucked wouldn’t even begin to describe his situation.

…Actually, now that he really looked at his situation, it seems he didn’t have ANY options.

He sighed as his situation sank in, then yawned, which surprised him—he hadn’t noticed between finding himself inexplicably alive after taking a nuke to the face, and stuck in the body of a xenobiologist’ wet dream, but he was mentally exhausted, the closest he could ever really get to feeling physical fatigue.

And with that thought, and with no answers forthcoming, Alex slowly made his way into the cottage, which looked as homey and warm inside as it did outside. Feeling his exhaustion weighing on him and just wanting to rest, he dismissed his observations of his surroundings and immediately began searching for the bed, which he quickly found on the second floor. Not thinking twice, he made to hop on to the mattress (a small part of his mind taking note of how similar it looked to the beds he was familiar with, if a little on the retro side, thus suggesting that the pegasus he now resembled might have had some previous exposure to humans) when the flash of reflected moonlight caught his eye. His head was already turning to look before it even consciously registered, and he was greeted with his new reflection:

The face that greeted him was, as expected, equine, though only just recognizable as such— the fur was the same shade of yellow as the rest of his coat, the eyes were binocular and blue and larger than any he’d ever seen on anything of similar size, the muzzle was smaller and shorter and seemed to be capable of emoting, if the tired, sad, and recognizable look his reflection was sporting was any indication, and his hair— or would that be mane?-- was pink and styled so that it curled in a lock over his face on one side, and flowed down his neck on the other side. Overall, the image presented was alien enough that it was adorable in the same way a puppy or a kitten was adorable, but anthropomorphic enough that it was also attractive, a contrast that Alex knew he should have found disturbing, but couldn’t quite bring up the willpower to care.

But that wasn’t what made Alex depressed, though. What sent a pang through his non-existent heart was that, even now, when the eyes staring out of that pretty face were those of a killer of thousands, there was still a measure of innocence there; whoever or whatever she had been before he’d gotten to her, she had been innocent in a way that was almost impossible in this day and age… and he’d killed and consumed her without a second thought. He’d known he was a monster, but here, looking in the mirror, at that innocent face with the killer’s eyes… it really drove that point home.

Alex sighed, and the image sighed along with him. “I’m sorry,” he whispered to the reflection, before turning away and finally hopping onto the mattress. He settled down and, when he was as comfortable as he could be sleeping on a dead girl’s bed, and got down to business. He needed to figure out why he couldn’t access this girl’s memories, and since he didn’t need to sleep, he figured he might as well put his extra time to good use.

He allowed his mind to relax into something akin to a meditative trance and, when his mind reached a certain point, turned—it was the closest term he could use to describe what his consciousness did. He took the familiar “route” to what he’d cheekily called his “Web of Intrigue,” the area of his mind where he kept all of his foreign memories.

It was both eternity and a mere moment before he reached his destination. When he emerged in the Web of Intrigue, he expected to see the familiar giant brain full of firing neurons that was its mental representation. And while the familiar “sight” was indeed what greeted him on his arrival, he was also greeted with something… else. Something that had him performing the metaphysical equivalent of gaping in shock.

…Well, at least he now had a hypothesis on what had happened to the pegasus’ memories…

A/N: …I’m sure everyone knows what happened. And yes, I realize Mercer hasn’t attempted to shapeshift back into his human body. He will attempt to, sometime in the next chapter or two—he’s still in shock at being in a body that has no right existing according to the rules of the universe as he knows them, so his priorities are a tad bit skewed at the moment. I’m also well aware that he’s a tad bit OOC. That will eventually be explained, though I’m sure, much like with that cliffhanger, many of you can figure out what happened.

Also, I'm looking for more beta readers. My current beta, Delta Shock, is awesome, but he's only one man, and I'm of the firm opinion that more criticism can only be helpful... as long as they're not useless flames, at any rate. So if you're interested, please leave either a private message or a note in the comments area below. Thanks!

Comments ( 21 )

Fuck it, I'll help ya. I got lots of experience with pre-reading. I remember when the first chapter of this came out, I LOVED it. Sometimes, people... ponies... need to die in order to progress a plot.

1579722 Sweet! Can you start with this chapter? As you've probably noticed, this one is unbetaed. I sent a manuscript to Delta Shock, but he hasn't replied yet, and I'm somewhat impatient at the best of times. Thank you so much!

Also, I'm available for beta services, as well, so if you ever need something pre-read, I can help! :twilightsmile:

1579746 Sweet. I was wondering what you meant when you said unbetaded. For starters it shout be un-betaed. Notice, the dash. Anyways, how do you usually do this?

1579776 Ah, thanks. Fixed. And I usually send the Word manuscript over to the pre-reader via e-mail, but if you prefer doing if from this site, that works, too.

1579783 Yeah sure. I'll send you my E-mail so you can send em to me.

1579789 Alright, thanks! Sending now...

Please don't take months to update this again because this has potential to be one of the better prototype crossovers.


No promises. I work really, really slowly, unfortunately. :applejackunsure:


...Good for you? Can you at least tell me why? :trixieshiftright:

SHEE LIIIIVVVVEEEESSSS!!!!!!!!!! maybe.....:duck:

I suppose this fic is dead then?

When flutter shy dies fans go to shit

Well, this is a new spin of a prototype crossover, a very interesting read. Hope you find the time and inspiration to continue it!

Is the momory block, because of the parasite thing that nearly killed Mercer in Prototype 1?

Fic is dead, not updated in 5 years

Nope. That became the Supreme Hunter, and the story actually mentions Alex killing it (which is Canon, BTB). My guess? It’s similar to when he consumed the ORIGINAL Alex Mercer. THAT was Alex’s first set of HUMAN memories. Fluttershy was (in-story) his first PONY (a PEGASUS, to be exact), so here’s my own ‘Hypothesis’; Each time Alex consumes the first of a new Sapient species, he has to ‘reconstruct’ or (to an extent) ‘recreate’ certain situations to recall his new form’s old memories. And seeing as Pegasi, Unicorns and Earth Ponies are different Pony Sub-Species (yeas, that’s a real life term), my guess is that something similar will happen (if to a (somewhat) lesser extent) when he consumes his first Unicorn and first Earth Pony.

Who ALEX MERCER WOULD KILL? Poor Fluttershy. :fluttercry::pinkiesad2:😢

Yup. Believe me, I’d kick his proverbial ass too, if I could. But still, at least he’s feeling some guilt about it, instead of none.

The brain also needs to be mostly intact when he eats it.

I agree.

Also, TheFanficStealer? When are you actually going to update the story? It’s been almost eight (8) years since the first chapter came out.

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