Prototype: New World, Still Hunting

by Dr_D

Rating: mature
Tags: Dark, Alternate Universe, Romance, Crossover
Length: 4421

After getting hit by the nuclear blast in NYZ, Alex Mercer lands in a world full of ponies. He now wishes he was capable of death.

Warning: This fic contains ponies with modern tech, for those of you who dont like that.

Alex Mercer saved Manhattan by bringing the nuclear bomb to the ocean, but when it detonated, Alex's instincts took over and sent him into an animalistic rage. When he wakes up, he finds things have changed. A lot.
Humanity is missing and ponies rule the world along with a few other species in their shadow.
Alex will have to adapt to the new world that moved on without him. He will succeed. Besides, it is what he does best.

Thanks to PyroCore and XSomeGuyX for editing.

Published 1970-01-01 00:00:00 UTC
Last updated 2013-12-01 02:08:09 UTC

Chapter 1: Wake Up, Eat Someone, Kill Some People. It's A Regular Routine.

When Alex woke up he felt a large pain in his head, the pain that comes from gaining new memories from his prey. Pushing the pain aside, opting to look through the memories later, he noticed two voices around him.

"So do we know exactly what this is?" A voice to his right asked.

"Well, its ability to change its shape suggests that it is a distant relative of the changelings, but changelings change shape magically." A voice to his left answered.

What the hell are changelings?

"They changed shape physically, perfectly mimicking the pony it is posing as, even on the inside. Making it invisible to detection spells." The voice continued.

And since when does magic exist?

"You know, this looks sort of like a human, like from that show." The voice on his right noted.

"You really watch that show? What’s so great about it?" The voice to his left asked.

"We can talk about all that after the dissection." The voice to his right stated.

They talk like they’renot human, time to find out why.

Alex sat up quickly from the table and opened his eyes, the sight that greeted him was not what he was expecting. The two voices where horses in Hazmat suits. They also had horns pointing from their heads which the suits also protected.

What? Did the nuke give me hallucinations?

Either I was unconscious a lot longer than I thought, or his is some blackwatch attempt to confuse me.

Deciding that he has no reason to continue wondering, Alex reached out with his hand and grabbed the horse to his left while the one to his right ran.

As he observed the horse struggling in his hand, he noticed something was trying to pry his hand off the horse. He saw a blue like glow surrounding his hand and the same glow surrounding the horn of the unicorn.

That explains the 'magic' they were talking about, but that still does not explain why these horses are sapient.

He looked to his right and noticed the other one ran off, and an alarm had sounded.

Alex got off the table, nearly collapsing as soon as he met the ground. He was weak, he needed to consume biomass. Alex looked at the horse in his hand who was still struggling in his grip.

Good thing I grabbed you.

He diverted biomass from his clothes to a tendril coming out of his side, which then imbedded itself in the chest of the horse. Alex then gripped his head in pain as new memories came into his mind while the horse he was once holding screamed in pain.

______________________________________________________________________________

“Doctor, what are we looking at.” Princess Celestia said from behind me.

“The future.” I said to her.

“As amazing as it sounds, the creature that has been rampaging through the world is capable of manipulating the cells in his body to be anything he wants it to be. So if it was not in a rampage, it would be able to blend in with our populations, make weapons with it’s hooves, and even take the form of others.” I explained.

“Biological tissue manipulated and transformed, on the fly.” I said with wonder.

“I need it on a slab I need to know what makes it tick.” I said.

“If I figure that out, we could cure diseases and disorders in ways we never thought possible, we could change what it means to be a pony.” I said.

“Before you can study it doctor, we want to capture it and see if we can bring out it's consciousness. If all else fails, we are going to kill it.” Celestia said from behind me.

“Of course, Princess.” I said.

______________________________________________________________________________

As the memory ended, Alex thought about what he saw.

I assume this ‘Princess Celestia’ knows about how I got here or how long it has been.

Suddenly Alex was struck from behind, he could feel the pain of bullets passing through him as the horse returned with security.

Ponies. He reminded himself. They are ponies.

He used his thermal vision to scan the room. And he noticed 13 ponies standing in the room watching the table he was hiding behind. Alex went back to regular vision and regenerated from the bullet wounds.

I need to be careful. A few more shots like that and I’ll be finished.

He then heard one of the ponies walking up to the table behind him. He got a hand ready to pull the pony to Alex's side of the table. As the head and gun of the equine poked into his field of vision, his hand shot up and grabbed the neck of the pony and pulled him down as he let go of his gun.

Alex then quickly consumed him as a tendril imbedded itself in the pony while blood gushing out of the wound. Alex pushed aside the new memories as the ponies once again opened fire on the table he was hiding behind.

Alex grabbed the gun of the pony he consumed and fired back at them. The sound of bullets hitting flesh and screams of agony sounded as his bullets hit their targets.

As the gun clicked empty, Alex turned on his thermal vision to see who was left.

There were three left, two soldiers and the scientist looking on the ground for something, probably for one of the guns.

Alex then shot up from the table shooting the two soldiers in the head before throwing the gun at the scientist, knocking him over. Alex ran to the downed doctor and raised his foot as small tendrils formed underneath it.

Alex brought his foot down on the scientist's head, crushing it as he was consumed. Alex shoved off the new memories as he figured out his objectives.

Priority 1: Get out of the facility

Priority 2: Regain strength in Everfree Forest

Priority 3: Asses the situation of Humanity and if needed, get a pony disguise.

The memories of the scientist told him that the Everfree Forest was not natural for pony standards, so he could hide there. There were also a lot of animals there so he could feed and gain strength. He knew some limitations the ponies had, but did not want to test himself in the condition he was in.

Alex started making his way up the facility killing and consuming security along the way, Alex thought that the entire building was underground so he went kept going up until he could not go up any further. This led him to the roof.

The building, twenty stories high, had a large military guarded wall around it with a gate. And pony military forces here pouring in from it. They had everything, tanks, APC's, attack helicopters and transport helicopters dropping in reinforcements.

Even with the increased biomass, Alex could not face a force that size, not now.

Alex thought about what he could use to take down that force with minimal risk, because he was not getting out until it was gone.

Alex then thought about the knowledge he had gained when he consumed Greene. He learned everything, how to create and spread a hive, how to control and take care of the hive mind and it's many hunters, and most importantly, how to adapt without consuming.

Basically, if he knew how certain biology could work, such as the magic the unicorns wield, without ever consuming one, he could make it his own without ever eating them.

Looking at the center of the small army, he had an idea. If he could unleash a weakened version of his devastator, that could destroy most of the force. He decided that instead of impale them; he could use the tendrils to bring everything closer to the center in a black hole effect.

Willing his arm to transform into a tendril, he pitched his arm back as if he was throwing a baseball, he then threw his continuously extending tendril at the center of the group. When it hit the center, the tendril penetrated the armor of the tank that was hit. The tendril stabbed the ponies inside and then more tendrils came out of their bodies, shredding the tank's armor and attaching itself to every other nearby object, pulling them in.

For them, it was chaos. Tanks crushing each other as they try to get closer, helicopters pulled from the sky’s, soldiers being pulled by something on their body as their screams died and everything exploded when fuel tanks were ruptured.

Alex smiled, the force was destroyed and there were no military bases in the area apart from the one he just destroyed, so he had free reign over the area to regain his strength. He jumped off the building towards the confused survivors.

Alex landed, forming a crater, he then took off towards the Everfree Forest before they had a chance to fire.

Time to let the forest know that I am the new apex predator.

Chapter 2: First Night In Ponyville

Alex was thinking about a pony disguise while on his way out of Everfree Forest.

As a result of his eight hour massacre against the creatures in the Everfree forest, Alex had enough biomass to take on armies with the power he now possessed. He felt unstoppable.

'But I still need a pony disguise, no need to bring nuclear weapons down on me.'

Alex decided to use the body of one of the security ponies as a base for his new disguise. The pony had bright red fur along with a short tail and mane. The mane and tail was black. Alex then checked the cutie mark and noticed it was a blue shield, on top of the shield was a heart the same color as his fur.

Alex then moved onto changing the body so he could not be noticed as one of the ponies missing from the base.

Alex first changed his fur into a deep midnight blue, he then made his mane and tail a bit longer and decreased the visibility of his muscles to make it seem he was never in the military. Alex did not change the color of his mane and tail as he already liked them the way they were. He then changed his cutie mark to a DNA strand, signifying the base of his abilities.

After finishing his body, he then walked up to a nearby lake to look at he reflection. While looking himself over, he noticed his blood red eyes. It was considered demonic possession in Equestria and was something Alex could never truly disguise . Nothing would help him hide those eyes when he walked the streets of Manhattan. The only thing that could hide them were his hood or a mask, and in Manhattan the entire population knew who he was and what he looked like. So that didn’t work, he could only use masks when he was in a military disguise. But here, nobody knew who he was and was free to do what he wanted without raising much suspicion.

Red and black tendrils then formed all over the upper body of Alex as he adapted his regular clothes to fit his new pony form. The tendrils slowly disappeared as a white shirt appeared, then soon after a gray sweatshirt with a hood appeared on top of the shirt, then finishing the look with his signature leather jacket. The hood concealed his eyes and made him seem a bit anti-social to any who saw him.

Alex thought back to the pegasi he consumed, the wings of pegasi required magic to hold them up. Something he could not use, but if he where to increase the size of the wings, perhaps he would gain enough lift to fly. As the familiar look of red and black tendrils formed on his back as he willed wings to grow on him. After the tendrils receded there were two large abnormally large wings on his back, the same color as his fur.

As Alex started flapping his wings, he noticed he felt a lot lighter, not enough to fly or even hover, but lighter than he was. Alex then started to shoot very small amount of biomass out of his wings, the amounts were so small he could not see it but after starting this, he started to rise from the ground as he started to fly. While he glided in a way similar to this, but here, he was not restricted by how much air time he had. He was truly flying.

'Let’s go back down now, no need to waste the biomass.'

After lowering himself to the ground he started on his way to Ponyville, a nearby village. So small that the population knows each other, but the population was also very trustworthy, and trust is what he needed from the ponies if he was going to hide from the military.

'Even if they do find out about me, it’s not like they can do anything about my presence.'

And with that thought, he raced off to Ponyville.

______________________________________________________________________________

When he entered town, Alex walked around town trying to find a place to spend the night while in ponyville. Alex stopped at a building that was labeled, “Ponyville Inn”. Deciding that this would be the best place to stay, he went through the front door and saw there was a mare at the front desk looking ready to fall asleep.

The room itself was nothing special, standard for most hotels or inns. A front desk with a small wall of keys behind it a few paintings or decorations here and there, with a elevator on the far side of the room next to some stairs.

Alex walked up to the front desk and said to her “Hello, I would like to rent a room.”

The mare looked up at Alex, “Ok, cash or card?” she asked.

Ales faked a sheepish smile “I don't have my card or my cash with me.” Alex said.

“Do you know your card number?” The mare asked.

Alex after bringing up the memory of one of the soldiers from the base said yes.

“Ok, please type it here.” The mare said after pointing her hoof at the screen in front of Alex.

Alex typed out the number then wrote the signature of the soldier with his hoof. Alex briefly wondered how pony hoofs could hold things but put that aside for later. After a few minutes, the mare handed Alex a key.

“Your room is number twenty two.” The mare said. “Enjoy your stay.” She said as he walked past her.

“Thanks.”

Alex then walked towards the stairs and started to climb to the next floor of the inn. When he got to the second floor, he started walking down the hallway of doors that were numbered from ten to twenty five. When he reached the door numbered twenty two, he put his key in the lock of the door and twisted it. This unlocked the door and Alex opened it.

The room was not anything special but it served Alex’s needs quite well. It had a bed, a window with blinds, a bathroom, a TV, a small kitchen and a calender on the wall that was on July.

The first day of July was marked with an X, meanwhile, the thirty-first was marked with the name; Summer Sun Celebration.

Alex closed the door behind him and locked it. He then closed the blinds to the window so nopony could see into his ro- 'Wait what?'

'Did I just say ‘nopony’?' Alex thought

'This place must be getting to me.'

After closing the blinds to his room, Alex laid down on the bed and started thinking about everything that had happened. The thought that dominated his mind was the state of his sister, Dana.

What happened to her while he was gone? Is she ok? Is she dead? These were the questions that went through his head, questions that he wished to have the answers to. Based on the fact that the memories of all the ponies in his head stated he had been a monster to Equestria ever since it was founded over four thousand years ago. So chances where, he would never see Dana again.

This did make him sad enough to cry but his next thought made him want to scream in rage.

'Karen betrayed me.' Was the thought that caused him grief when he thought about his past before he was infected.

Karen and him had been deeply in love, he cared about her almost as much as he cared about Dana. But he lost his memory when he was infected, he had no idea how much he truly cared for her. That’s why he was not that phased by the fact that Karen betrayed him when Captain Cross found him in the hive. But when he regained his memory on day seventeen of the outbreak, he almost cried as his just rebuilt heart broke from the fact.

But he was also furious and would later go and consume Karen on day eighteen of the outbreak, but dooming her to eternal existence inside his head did not calm him down, the thought still made him angry even today.

Deciding to go to sleep for the first time, Alex closed his eyes and willed his brain to enter the sleep cycle. As Alex did this, he had only one thought.

'Maybe after finding information about Celestia, I can finally have a normal life.'

Chapter 3: Day 1 In Ponyville

Alex found himself in the White House with a suit and sunglasses on.

‘How the hell did I get here?’ Alex thought.

Alex then felt his body move by itself looking as he noticed a black man, also in a suit who was being escorted by service agents down the hall. He looked toward a barricaded door that was being pounded on by something. He then put his hand in his ear.

“HQ, where is that evac? We can't hold them forever!” his body said on it’s own.

Alex then heard a response: “Agent, a transport chopper is on the way. Just keep president Obama safe until evac arrives. Bombers are going to commence bombing of D.C. as evac gets there.”

Then thoughts, not his own, entered Alex’s mind.

The eggheads said that the virus had been eradicated in New York 6 years ago, then it pops up in Brazil and becomes global with confirmed cases in every country on Earth. Most of both American continents are in anarchy,with the US just barely holding on. Meanwhile, Europe and Asia have mostly collapsed while Africa has no human life at all. With about 6 billion infected and turned into the fucking zombies,banging on the doors of the White House,and most countries gone, some people have lost hope and committed suicide as others attempt to escape to Antarctica or Greenland… But atleast the politicians finally agree on something: We need to escape.

The thought finished just as Alex heard something rumble behind him. As he turned around and he recognized what he saw as the hunters from Manhattan, one jumped at him and his vision went dark.

______________________________________________________________________________

Alex immediately sat up in bed. He began to think of what he just saw and the implication of those memories

‘Ok, so something happened to me when the nuke went off.Most likely I was in some sort of animal rage, consuming things with no thought,or I would not have these memories. While I was in that state, my Blacklight virus caused a worldwide pandemic, possibly causing humanity to go extinct. But that raises the question: where are the human continents? The continent that Equestria and the other nations are not on a landmass that existed onEarth. And there are no continents from Earthon the ponies maps. Perhaps Celestia has some answers, and the upcoming Summer Sun Celebration is the perfect time to ask,’ Alex concluded.

Alex then noticed his forelegs; they had shifted into claws. Alex willed them to revert into their pony form. Alex watched the large pulsating arms that ended with three large, blade-like claws become covered in a mass of red tendrils as they shifted to blue stumps that were hooves.

Alex looked to the clock on the wall; it read 6:25 in the morning. Alex opened the blinds and noticed the sunrise on the horizon with only shop owners were outside.

Alex got out of bed and opened the door to his room. Walking out and shutting the door behind him, he eyed at the walls of the hallway he was in. Nothing had changed and probably never will.

Walking down the hallway and down the stairs, he found that there was a different pony at the front desk then last night. His strange clothes earned Alex a few curious looks from the ponies in the lobby, but they quickly turned their attention back to their own business as he walked passed them.

Alex opened the front door to the Inn and walked outside. He immediately felt the warm summer air on him, a noticeable difference the the cool air conditioning of the Inn.

‘Well, probably best to go to the library to figure out Equestria’s history. There were not any historians at the base I consumed’.

With a destination is mind, he set on his way to the hollowed out tree he saw last night. As he walked,, he noticed many ponies were staring at him, as he expected they would. But one pink pony gasped and sped away with an agility nearly matching his own. Alex starred where the pony once was.

‘Ok, nevermind the fact that my clothes brought that kind of reaction. What I want to know is how she ran so fast,’ Alex thought with confusion.

Shaking the thought off Alex noticed a rainbow coloured tail poking out of a low flying cloud. Deciding to deal with the failure of a spy, he ducked into an alleyway so the pony lost sight of him, Alex then quietly flew up behind the pony on the cloud who had stuck its head out to look for him. Alex noticed that the body structure of the pony was that of a mare and that she had cyan fur.

‘Rainbow Dash, of course… How did I not recognize you from the tail,’ Alex thought, immediately recognizing the pony.

Closing his eyes, Alex brought up a memory of the officers at the base the contained Rainbow’s file;

______________________________________________________________________________

“Dash, Rainbow. No next of kin. Father: Rays, Spectrum. Status: Alive, currently living in Cloudsdale. Mother: Dash, Fire. Status: K.I.A. Died in wonderbolts training accident,” I read aloud to the other officers in the room.

“Captain of the weather team in Ponyville, she should be contacted if we want have certain conditions during our operations. She is known to be lazy and put off jobs till last moment, she gets jobs done faster than most of the weather team combined,” I continued to read.

“Survived an encounter with the creature due to our assets arrival in Cloudsdale. Lived under observation with her father after the creature escaped the area. She is very inclined to meet or find the creature due to this.

“Loyal to Equestria’s military. Specifically, to the Wonderbolts. Will do almost anything we say.”

“She is to be protected for reasons classified R.A.ONE,” I finished.

______________________________________________________________________________

When Alex opened his eyes, he was not surprised to see Rainbow still looking for him, experiencing memories only took two or three seconds in real time after all.

‘I wonder why she needs to be protected. R.A.ONE means Celestia and only Celestia can view the info. I guess that’s another thing I will find out when I consume her,’Alex thought.

Alex grabbed Rainbow’s tail and pulled her off of the cloud.

“Woah,woah! Ok! I am coming out, just let go of my tail,” Rainbow said.

“Why were you spying on me?” Alex questioned her.

“Um, um,” Rainbow stuttered as she tried to come up with an excuse.

Both hovered there for a few minutes as Alex waited for an answer to his question, as Rainbow continued trying to figure out a excuse.

“Ok, so I caught you red hooved. I am willing to let this go if you can point me to a potential job,” Alex sighed. Alex did not need a job due to the fact that he had the bank accounts of many of the ponies, however simply sitting in his room until the celebration without doing anything would raise suspicion.

“Well, my friend Applejack is looking for some help on her farm, and we can always use a few extra hooves on the weather team,” Rainbow replied.

“Applejack’s farm is that way,” Rainbow said while pointing towards a large orchard in the distance.

“If you want to join the weather team, meet me at my place,” she said while pointing to a floating house made of clouds on the edge of Ponyville.

Rainbow started to fly away but stopped suddenly and turned to Alex.

“Oh, and what’s your name?” Rainbow asked.

“Alex Mercer.”

“Kind of weird name, but also kind of cool.” Alex heard her say to herself.

“Well, ok then, Alex. I'm Rainbow Dash, see ya later!” Rainbow said as she flew away.

Alex flew back down to the ground and began to plan his next course of action.

I could go and accept the job for the weather team, but then I would be working water for extended periods, vaporized water yes, but still water. Or I could take the job at the orchard, but that would use up most of my time. Or I could go to the library to read up on Equestria’s history.

What to do next...

Prologue: Instincts

"...Only I know the code..."

The wet sound of meat being smashed and crushed. A blur of images. Daylight. Panicked shouts and the thud of boots, almost drowned out by wailing alarms.

"...Deck! All Hands on Deck! Intruder..."

A monster, easily twenty feet tall, squaring off against a black shelled humanoid creature. The roar of planes and the sharp crack of firearms filled the air, followed by the dull thump of bullets cracking into flesh.

"...All available support to Citadel..."

The roar of engines and great rolling explosions. The screams of a beast in pain, and the dull slurping sound of something burrowing through flesh.

"...Father Device has been activated..."

A panicked rush, the rough feeling of chains, the noise and lift of something heavy moving through the air.

...Speed…

...Noise…

...Light…

...Heat…

…

PAIN!

PAIN! PAIN! PAIN! PAIN!

REGAIN STRENGTH! HUNT! KILL! CONSUME!

HUNT! KILL! CONSUME!

Hunt... Kill... Consume…