Equestria Effect: Apocalypse

by ProtheanBrony

Rating: mature
Tags: Romance, Adventure, Crossover, Human, Alternate Universe
Length: 2021

After the Normandy SR2 crashes into an unknown planet, what happens to the crew?

ME3 Ending Spoilers- Which nobody cares about.

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When the Normandy crashes on the unknown planet, what happens to the crew on board at the time? And what happens to Shepard back on Earth after defeating the Reapers? His quest to reunite with his squad leads him to the planet where they are marooned…

Equestria.

I am writing this as if the Indoctrination theory was true, but the Normandy, for reasons to be explained in the story, still flees with the squad.

Published 1970-01-01 00:00:00 UTC
Last updated 2012-04-27 06:14:03 UTC

Chapter 1: Isolation

Hello everypony!  I will be deviating from the crap that EA/Bioware calls "Canon" a bit, such as more than 4 people being on the Normandy as it leaves the fight.  Oh yeah, spoilers, but F**k that, becuase the "Canon" ending sucked.  As in the description, I am using a Indoc Theory/Canon Mix.  Yay.  Listen to me rant.  Now read.

"Shit Shit Shit!"  Jeff "Joker" Moreau cried as the Normandy was drawn into the unidentified planet's gravitational field, and with even the emergency backup fusion batteries offline, he had no control.  The only thing he could so was transfer the remaining power into the charge of EDI's mobile platform.

"Jeff, I have calculated our chances of survival.  Under these circumstances, it is about 1.4 in 1,504,324,318.  Then again, that is with full power and shielding.  Without it, it is about .09 in over a trillion."  EDI replied, a hint of emotion in the unleashed AI's normally dull, monotonous voice.

"EDI, that is a high enough chance for me!  Are the emergency thrusters online?"

"Jeff, all other systems have been disabled, and are leeching their power into my mobile platform.  Why?"

"I have no idea where we are, and I need you EDI.  I need to keep you alive as long as possible!"

"Mr. Moreau, I am aware of your affection for me, but this is irrational.  You must disable the emergency override on the backup thrusters."

"EDI, no!  I can't let you die, too!"

"I am sorry, Jeff."  EDI then activated her mobile platform, draining its already minuscule batteries.  With her last strength, she shoved Jeff out of the pilot's chair, probably breaking his arm and a rib or two.  She flipped open the cover for the emergency power diverter override, and hit it.  She took control of the thrusters, and re-angled their entry position.  She turned, and approached Jeff.

"It was necessary, Jeff.  I am sorry.  I... love you." and her metallic corpse clanged against the bulkhead, and slid down, as the last of her power supply was drained.

"EDI! NO!"  Jeff cried, and pulled himself to her body.  "No! No! NO!"

Garrus Vakarian rushed up the emergency maintenance vents, trying to reach the bridge.  The Normandy's hull was breached throughout the entire hangar, instantly killing James and Cortez, and sending their Hammerhead and Shuttle hurtling into the vacuum of space.

"Come in!  Anybody?! This is Garrus!"  He continued up the maze of ladders and vents towards the bridge, when the he got a response.

"Garrus!  Thank the goddess you are alive!  I'm trapped in in the Command Center!  Javik and Tali are with me, but Javik is wounded!"  Dr. Liara T'Soni said, as a large explosion was heard.

"Shit! I think the Engineering deck was just breached!  Agh, fuck!  Crawling is another think Turians aren't supposed to do, along with swimming, singing, cheerlead-"

"Garrus, forget that, just get up here!"  Liara complained.

"Alright, alright, calm down, I'm in Life Support right now."  Garrus replied.  He continued through the tunnels, grunting and complaining to himself, and reached the bridge, where he shoved some supply crates and miscellaneous debris out of the way, and sprinted to the Command Center.  He hacked the sealed door open with his Omni-Tool, and was appalled by what he saw.  The pair of ensigns manning the security checkpoint were both dead, crushed beyond recognition by numerous cabinets and the security scanner.  As he rounded the corner into the Conference Room, he found a pair of dead Quarians.  Admiral Daro'Xen, and her bodyguard Kal'Reegar were crushed under the collapsed table, with the class panes surrounding the room were shattered, and apparently exploded from the force of the explosion's shockwave, spreading the shrapnel into the occupants of the room.

He hurried into the Center itself, and found Engineers Daniels and Donnelly, with no sign of Adams.  Behind them, in the QEC chamber, was Tali, trying to establish a connection on the communicators, along with Liara, who had a pair of large slashes along her thigh, leaning over Javik, who was in a puddle of his fluorescent green blood.  He seemed to have been hit by a girder that fell from the ceiling, leaving him with a deep gash in his lower back.

"Garrus, thank the goddess you made it.  Javik should be fine, if we can get some proper medical attention.  It is not as serious as it looks, but his biology has forced him into a trance-like state due to the blood loss.  Try to find Chakwas, she was in the CIC with Traynor and Joker!"  Liara ordered.

"Got it, I'll be right back!"  Garrus said, and backtracked to the CIC.  He retrieved his helmet as he passed a supply cabinet he had stored it in last night before helping Tali "calibrate" her suit.  He was grateful for her survival.

Joker was in shock, just kneeling over EDI's body, oblivious to the chaos around him.  He was acting robotically, a bit like EDI did when he first met her.  He pulled himself up, and approached the Cockpit containment shield, which was normally used to keep the Cockpit pressurized when the rest of the ship was breached.  He planned to use it differently.

Garrus stormed into the CIC, where he spotted Traynor, crushed by the collapsed command terminal.  Chakwas was near her, pinned by a large piece of debris.

"Garrus! Over here!" she called.  Garrus approached her, and lifted the debris, as she pulled herself out from under it.

"Head to the Command Center, Javik needs help."  Garrus said, and sent her on her way.  He headed towards the Cockpit, where he spotted the a glimmering azure barrier in his path.

"Joker! EDI!  You in there?"  He queried.

Joker heard Garrus, he didn't care.  He approached the emergency manual ventilation controls, and flipped up the cover labeled 'Cockpit'.

Garrus pounded on the containment shield between himself and Joker, to no avail.  He could only watch in despair as Joker approached the airlock controls.  His predatory vision caught sight of a metallic corpse in the corner.  Oh, shit.  The holopanel lit up, and Joker accessed the venting controls.  Garrus shouted, pounded, even tried overloading the door, but Joker just remained oblivious and jettisoned the contents of the cockpit into the atmosphere.

The Normandy was descending extremely quickly, EDI thought to herself.  Only a thousand more meters until impact.  Her sacrifice has granted them an additional 5% chance of survival.  That was as much as she could do.  She was beyond repair, the EMP wave from the explosion wiping her backups, and draining her entire reserve power supply.  She diverted her final power to the shields, and the faint whir of her main core ceased.

The Normandy violently impacted the earth, and skid across the lush greenery, leaving a trail of burning debris.  It came to rest at the edge of a cliff.

The survivors clambered their individual ways out of the Normandy's husk.  Garrus, Liara, Tali, Chakwas, Donnelly, Daniels, Javik.  They all stared into the distance in unison, at a peculiar city built into the side of a mountain.  It was colorful, maybe too much so.  It had numerous spires jutting from its otherwise relatively flat layout.

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Princess Celestia knew something was wrong.  The last time a meteor that size arrived... it was carrying them.  The Reapers.

Chapter 2: Assimilation

1 Hour Ago, Ponyville, Equestria

Twilight Sparkle could only watch in horror as the gargantuan bipedal... thing approached.  It seemed to be a massive mound of muscle, flesh, and cybernetics, with a terrifying skull of some kind of alien acting as its head, supported by an uncharacteristically skinny... Oh, God, it was a bare spine!  It was smashing down doors and barricades with ease, and nothing could stop it.  It was gradually inching closer and closer to the library, and Twilight was very unsure that the bookshelf she had blocked the door with would hold.  Every time it reached a house, it smashed down the door, and one of the sacs on the giant, bulbous insects burst, and a swarm of some kind of larva poured into the house, traumatizing screams coming from every pony taken.

She watched in horror as first Sugarcube Corner was broken into, then Lyra's house, and finally they swarmed the market, taking the oblivious ponies by surprise.  The bipedal hulk was rapidly approach the Library.

"Oh, what are we to do!" said Rarity.  She, Twilight, Rainbow Dash, and Pinkie Pie were all hiding inside the hollowed out tree.  Applejack was harvesting Zap Apples when the monsters arrived, and Fluttershy was captured when she tried to befriend them.

"AGH! I don't know! We are going to die!  I haven't even joined the Wonderbolts yet!" Cried Rainbow.

"Just, don't worry!  The princesses will be here any minute!  They can fix this!  I hope..."  Encouraged Twilight, when suddenly,  BOOM!  BOOM!  And the bookshelf holding back the monsters was toppled, the strange larva skittering over it.

"Oh, they look so filthy!  Just... Hideous!"  Rarity whined, as she retreated up the stairs.

"ALRIGHT YOU PARTY POOPERS, TAKE THIS!" Cried Pinkie, as she pulled out the party cannon, and fired it.  The normally friendly, welcoming, fun party supplies each gained deadly attributes.  The confetti shot out, like razor blades, flying towards the swarm of larvae.  The pin-the-tail-on-the-pony sets each had sharp pins on the tails, arching across the room like bullets.

"YEAH! TAKE THAT! Yeah! Yeah.... Uh-oh."  Pinkie said, as she noticed that the cannon had done nothing but add festivity to the soon to come massacre.  Then, the swarm washed over her, cocooning around her, and carrying her outside.

"Pinkie! No!"  Twilight cried, and the horde turned around.

The Apple Family had founded Ponyville; they weren't going to let these scoundrels take it away from them.  Mounds of dead Husks, Marauders, and even a Brute were stacked outside the Farmhouse, like a warning to the rest of the creatures.

"Whew!  That thing sure was tough, right Big Mac?"  Applejack inquired, tiredly.

"Eeyup."  Big Mac said, splattered in the blood of the monsters he had killed.  But they were running out of weapons.  The last of their homemade Combustible Lemons were gone, and all they had was some pitchforks, a shovel, and some barrels.

"I wonder how the rest of the girls are doing..."  Contemplated Applejack.

"Rarity!  You have to!  This is our best chance to remain undetected!"  Ordered Twilight.

"I refuse to roll in this mess like... a dog!  It shall simply ruin my mane and coat!"  Complained Rarity.

"Really! This is a matter of life and death, Rarity!  You have to!"  Twilight argued.  Solemnly, Rarity steeled her will and stepped into the spread of blood and gore that had been left behind when Twilight dropped a bookshelf on a crowd of the beasts.  She knelt down, and rolled.

"AGH!  THIS IS DISGUSTING!!!"  Rarity burst, attracting the attention of the remaining horde.

"Rarity!  Agh!  Quiet!  You'll attract-" Twilight was interrupted by a large Caterpillar-like creature with wings smashing through the roof of the Library.  It shot a pod down into the floor, and flew away.

"Well, that was harmless.  So lame. Hehe."  Said Rainbow, nervously.  Then they swarmed out of the pod like a flood.  Dozens of Larva skittered forward and engulfed Rarity.

"MMPH!  MMPH! MM-"  Rarity's screams were cut short when the larva sprouted wings and took to the air.

Applejack was rushing into town along with Big Mac and the "CUTIE MARK CRUSADER MONSTER SLAYERS YAYs!"  All she had was a pair of pitchforks strapped to her saddlebags, and Big Mac had a large barrel of molten molasses mounted to his back, with a hose in his mouth connected to it.  The CMCMSY!s were just cowardly hiding behind them, the poor fillies.  Applejack had finally left the Farmhouse after the monsters had broken through and Granny Smith had to sacrifice herself to let them escape.  They were charging towards the Library, passing by hordes and hordes of monsters on the way.

Twilight Sparkle was desperate.  For all she knew; only she and Rainbow Dash were alive.  Rainbow was carrying her over the Everfree Forest, towards Canterlot.  They needed to reach the Princesses; make sure they were safe.

Garrus Vakarian was tired, pissed, wounded, and worst of all, hungry.  Between him and Tali, they were running very low on dextro-amino acid supplies.  He was just as likely to starve to death as kill a Reaper with his bare claws.  They were about a mile away from the strange city he had spotted earlier.  Worst yet, they had encountered Reaper forces here.  But something was... off about them.  They seemed... uncoordinated.  Lost.  Confused.  But still just as deadly.  They had encountered a new kind of Reaper, as well, which meant that some kind of new alien race was present here.  And that is when they spotted it.

Javik was just regaining consciousness; that is when he thought he was dead, because he recognized the symbol in the sky; the Sonic Rainboom.