War of the Reapers

by Caladis

Rating: mature
Tags: Science Fiction, Profanity, Mass Effect, Violence, Crossover, Alternate Universe, Human, Narcotics, Twilight Sparkle, Drama, Gore, My Little Pony: Friendship is Magic, Other, Adventure, Sex
Length: 2774

Commander Shepard enlists Princess Twilight Sparkle's help to defeat the Reapers before they can destroy the Galaxy.

Set in Mass Effect 3, in an alternate universe where Ashley Williams and Kaidan Alenko both survive Virmire from the original Mass Effect and everyone survives the suicide mission from Mass Effect 2.

(Fans of the game series will know exactly what I'm talking about. Story includes some spoilers from the game if you've never played it.)

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The Reapers have arrived and it's the end of days... yet the Ponies of Equestria... of all creatures, might can save the Galaxy if Commander Shepard can convince them to help.

Princess Twilight Sparkle has lost everything but she's willing to help... even if it costs her soul. Blood, sweat and tears will be shed... but romance can bloom in-between battles, if everything works out.

When tomorrow is not guaranteed, today is all we have.

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(This is an epic story that I honestly probably will not finish. It's too ambitious for me but I can't help myself. Inconsistent chapter updates shall ensue. You've been warned!)

Published 2024-03-02 21:50:01 UTC
Last updated 2024-03-02 21:50:01 UTC

Chapter 1 - Equestria Fallen

Commander John Shepard had his orders. As the only son of Alliance Navy parents, and as a Navy Officer himself, he had followed orders his whole life. Some he liked, some he didn’t. This new mission was… unusual, especially given the current state of the Galaxy. It felt like a waste of time, not that he could really complain.

Nobody had listened to his warnings, but he had been right all along. It was too late to tell them ‘I told you so’ and he was too professional to have done so even given the opportunity, but Admiral Anderson had always been willing to trust what he had found, if only because it was a big galaxy out there and truth could be stranger than fiction.

Old secrets. Old weapons. Secret plans. Cover-ups of all kinds. The genophage that the Salarians created and the Turians used against the Krogan would have been considered War Crimes on Earth in the World War II era, but for the Citadel Council, it was business as usual. The fact that the Protheans had been wiped out during a galaxy wide war against giant sentient machines made more sense than them simply vanishing without a trace, and yet, nobody had wanted to believe it.

Earth had fallen to the Reapers. It was unsurprising given that the Earth Alliance had one of the smallest Galactic Navies of the great powers of the Council races. Maybe Earth would have been ready if they hadn’t taken so many losses fighting pirates in the Verge, losses from fighting Cerberus or losses from fighting the Collectors. Maybe the losses they suffered protecting the Destiny Ascension in the Battle of the Citadel was the hardest to accept.

Deep down, Shepard knew that the Geth fleet that had aided Sovereign tilted the balance against the Citadel defense fleet but if the most powerful Dreadnought in existence couldn’t take down a single Reaper Dreadnought… the Galaxy was in trouble. The recent Reaper invasion proved that Dreadnought sized reapers were rare, but Reaper ships outclassed similar sized ships in every category. It took a Destroyer to stand any chance against a Frigate sized Reaper. It took a Heavy Cruiser to stand a chance against a Destroyer class Reaper. It took a Dreadnought to take down a Cruiser sized Reaper, and thanks to the Treaty of Farixen, there was a severe limit to the number of Dreadnoughts in existence. The losses taking down a Dreadnought sized Reaper were extreme and so far, they had nothing to even the odds. Probably too late to design a Super Dreadnought.

It had been roughly 3 years since his original mission to take down Saren, the rogue Specter and his reporting of everything of any importance to the Alliance Navy High Command and the Council. The lack of additional Planetary defenses or increased warship production was troubling. As many ships as the Reapers had hit Earth with… it might not have mattered much but it would have been nice to be able to have put up a better fight. Given how the Reapers had made their warships, every ship lost was truly a loss for them… and they had lost far too few taking down a major Galactic power.

Additionally, the Mars Scientific Outpost had been attacked by Cerberus, which was, in hindsight, also unsurprising now that the Reapers were attacking in full force despite Shepard having defeated the Collectors. It wasn’t a good time for humanity to be divided, especially since Cerberus was just as well organized as the Earth Alliance Navy as far as having well trained personnel were concerned, even if they didn’t possess as large of a Navy. Every life lost fighting each other and not the Reapers was another step closer to being wiped out.

His ‘Specter’ status was intact, and he retained his Earth Alliance military rank even after his mis-actions while serving with Cerberus. Admiral Anderson remained a steadfast ally. Having just left the Citadel, he originally had wanted to go straight to the Turian Homeworld of Palaven to find Garrus and help with repelling the Reaper advance, but he had other orders to follow first.

Apparently, there was a biotically advanced race of sentient ponies on a Council classified planet only known as ‘Equis’ that might be able to help with the war effort against the Reapers. Reapers appeared to be weak to biotics and Equestria’s ‘Unicorns’ could help turn the war in the galaxy’s favor if they could get Princess Celestia to join the war effort. The Council’s records were a little old, given that no one visited the planet often to maintain its secrecy, but there was hope that the Equestrians would aid in the war effort.

Sitting in a briefing room, Shepard looked at his team and looked back at him eagerly awaiting the briefing he needed to give them before they landed at their classified mission destination.

He had served with Kaiden Alenko since the original mission to Eden Prime to recover a Prothean beacon on the original Normandy and they had saved Ashley Williams from the Geth during that same mission. After that first mission, they had been near inseparable, becoming close friends with each other despite the difference in their ranks, Williams having been a Gunnery Chief and Alenko having been a Lieutenant at the time. 2 years later, after technically being dead or at least comatose and some time apart working on separate missions, Cerberus of all organizations had saved him and even built a new Normandy to replace the original one that had gotten destroyed. Reunited with Shepard’s return to the Alliance and having turned over the Cerberus-built Normandy to the Alliance Navy, they all managed to flee Earth together after the Reapers attacked. Ashley was now a Lieutenant and Kaiden was a Lieutenant Commander, though they had earned those ranks themselves. The only sore part he had was that he himself was still just a Commander despite being the commanding officer of the Normandy. Being a Captain officially would have been nice, though it might be strange to be the same rank as his mother, since she kept refusing promotion to Admiral. He was worried about her though, given that she commanded a Frigate like his own, and they just weren’t a match for Reapers unless they were formed into wolfpacks of 4 to 6 of them attacking Reapers at the same time, and even then, it would be risky for a frigate to attack anything larger than a destroyer.

That line of thought forced him to recognize that he almost lost one of his current team in a previous mission, The Battle of Virmire.

Shepard’s Specter status and the causal practice of recovering enemy weapons and armor during the dozens of little battles they had while trying to find Saren had given the Normandy quite the stockpile of extra equipment. Careful planning and upgrading the onsite Salarian Special Tasks Group with better weapons and armor along with good execution of the agreed upon plan allowed both of them to survive Virmire in a situation where realistically one of them should have died. A lot of the Salarians didn’t make it, even with the equipment upgrades, though he was happy that both of his friends survived.

Shepard cleared his throat. “Okay, I’m going to give you both a classified briefing about what to expect when we arrive at Equis. I’ll admit I read the reports twice myself… and this one is a little far fetched even by the standards of what we’ve already seen.”

Ashley snorted. “Give us your worst, Shepard.”

Shepard smiled at her. “The planet consists of sentient versions of creatures from Earth mythology. There are intelligent and talking Dragons, Griffons, Minitaurs, hippogriffs and the actual target of the mission… ponies. Specifically, Earth Ponies, Pegasi and Unicorns.”

Ashley blushed. “Okay… that’s on the weird side.”

Kaiden jumped in. “So… we’re going to negotiate with talking ponies?”

Shepard nodded. “Yes. On the Planet, Equis, the pony nation is called Equestria, and it’s ruled by an Alicorn. And before you ask, an Alicorn is basically a combination of all three pony tribes. They have the physical strength of Earth Ponies; they have wings and can fly like Pegasi, and they have a Unicorn horn and can cast ‘magic’, which we would probably call biotics. At last report, the ruler of Equestria was Princess Celestria. She is described as having a white coat and multicolored mane. She has a sister named Princess Luna who is also an Alicorn and has a Navy-Blue Coat and matching mane. There is also a Princess Mi Amor Cadenza, who has a pink coat and multicolored mane. Finally, the newest Alicorn was reported to be a Twilight Sparkle, who has a purple coat and a purple and pink mane. Those four ponies are the most powerful ponies alive, both ‘magically’ as well as politically. Even with the existence of other nations on their planet, they more or less rule the entire planet. What we are after is the support of the unicorns… specifically, the ‘Battle Mages.’ If we can get a few thousand of them… it might help turn the tide of certain battles. Any questions?”

Ashley shrugged. “Should pack extra carrots for the negotiations?”

Before Shepard could respond, Joker had managed the Mass Effect jump with no issues and issued an update.

“We have arrived at Equis, and we are landing in Equestria. The Reapers have definitely already been here but there are no signs of active Reapers at the moment. Preparing to set down on the Celestial Plain near the capital of… uh, Canterlot. Geez, what a name. Get ready for a hike to capital and be sure to pet some ponies for me.”

Leave it to Edi to spill classified information to Joker. Shepard snorted. “Of course, Joker.”

Ashley Williams and Kaiden Alenko looked at him. “How shall we gear up, Commander?”

Shepard thought about it. “This is a diplomatic mission but according to the records, Princess Celestia understands what Specters are, so going in armed shouldn’t be a problem. Gear up like a normal combat mission and let’s go.”

They departed in the Mako armored vehicle and headed straight for the main gates of the Equestrian capital.

Ashley called out to the team. “Reading signs of destroyed Reapers all around us. There are at least 20 Frigate sized Reapers that have been destroyed and thousands of dead husks and cannibals on the battlefield.”

Kaiden whistled. “20… damn. That might be better than our defense fleet did at Earth. Maybe these Unicorn biotics are worth trying to bring into the war after all. The Unicorns must be as powerful as Asari Commandos at that rate… they can really fight.”

Shepard shook his head. “I’ll take all the help I can get. Let’s keep going, slowly, and be on the lookout for active husks or cannibals.”

Kaiden nodded as he kept his eyes on the scanners while continuing to drive. “If husks are humans turned into Reaper troops, what are the cannibals?”

Shepard rubbed the back of his neck. “If I had to guess, they are what’s left of the Batarians.”

Ashley snorted. “I can’t say the Galaxy will miss them. Batarians were the worst pirates and slavers in the Galaxy.”

Shepard shrugged, not wanting to tell her that she was wrong but threw out his own comment. “If you think cannibals are rough, I’m not sure I want to see what Turians and Krogen turn into.”

That comment silenced conversation as they continued to drive through the deserted streets of what was once a busy capital city.

Kaiden commented. “No signs of life in the city proper. Reading a single life sign in the Castle. I guess it could be the Princess?”

Shepard nodded. “I guess that’s where we need to go then.”

As they pulled up to the Castle and disembarked the Mako, they looked around for any clues about the recent battle. Outside the Castle gates, there was scorched golden armor, spears, swords and crossbows. But no ponies.

Ashley scanned the area. “Dead Reaper troops are all around us, but no ponies?”

Shepard sighed. “Neither of you were with me while I was working with Cerberus to stop the Collectors. Reapers seem to leave their own dead, but all others seem to be dragged off to be melted down into some bio-gel and used to create a new Reaper, as the findings from Cerberus prove. I could wonder if that proves how valuable the ponies are?”

Kaiden didn’t want to think about it but cracked a joke to ease the tension. “A Pony Reaper would be entertaining to see. I suppose the laser beam would come out of the horn of a unicorn model.”

Ashley snorted. “Would an ‘Earth Pony’ model Reaper simply buck the enemy warships?”

Shepard chuckled at the mental image but clarified. “The Human Reaper we destroyed at the Collector base shot laser beam pulses from its mouth. The only structural weaknesses that our weapons could damage were a small piece on the chest and maybe the eyes. I’d wager that an Earth Pony Reaper would work the same way.”

Making their way through the castle was daunting. The empty hallways and the overwhelming silence were eerie at best and just plain creepy at worst. Unlike a lot of other ruins that the team had experienced over the years, the Canterlot Castle still looked like brand new, as if the fighting didn’t make its way inside these hallowed halls, and that made its total abandonment feel even more wrong to their senses.

Coming up to a set of golden doors brought them up short. Kaiden looked at Shepard. “The pony is beyond these doors. Orders, Commander?”

Shepard looked at his team. “We don’t know who is in that room. No matter what happens, take no hostile action. I trust that our shields and armor will hold until I can negotiate with them.”

Ashley nodded. “I suggest we put away our weapons. Just holding them might provoke hostile action.”

Shepard nodded and placed his weapon in its proper holster. Opening the doors, they walked in. Their eyes widened in awe of the beauty of the pony sitting before them.

Sitting on the throne was Twilight Sparkle. Her eyes were closed, and her head bowed down in sleep. Shepard’s team approached slowly and quietly. Once they were halfway to the throne, Twilight’s head rose from sleep, and she opened her eyes to reveal a pure white biotic aura.

“I shall destroy all enemies of Equestria. Speak now or be destroyed!”

Ashley went for her weapon, but Shepard stopped her. “I’ve seen eyes like those. They remind me of an Asrai Justicar I worked with. Pure biotic power.”

Out loud, Shepard spoke. “I am Commander John Shepard, a Council Specter. I seek the chance to speak with the ruler of Equestria.”

Twilight’s eyes ceased to glow as she managed to come down to a normal level. “Council? Oh, I remember Celestia telling me about that… I am the ruler of Equestria… Princess Twilight Sparkle. How may I help you, Spector?”

The change to a normal dialogue was off putting but Shepard rolled with it. “The Reapers are trying to destroy the Galaxy. We could use some Unicorn Battle Mages to even the odds if Equestria can offer some support.”

Twilight slumped on her throne. “I’m afraid that you are too late then. I am the last pony in Equestria. They… the Reapers, as you call them… took everypony. All my friends, my mentor, everypony… I am the last pony alive.”

Kaiden and Ashley gasped as Shepard walked forward towards the throne. He wrapped Twilight in a hug. “I’m sorry. Everybody in the Galaxy is suffering. If you are alone here… you could come with us. We could be friends. There is room on my ship for you and you can get your vengeance on the Reapers firsthand, if it pleases you.”

Twilight’s eyes sparkled with tears… “Friends? You would be my friend?”

Shepard nodded. “All of us would be honored, Princess.”

Twilight returned the hug. “I would be happy to be your friend and I would be happy to help you defeat these Reapers. Please… call me Twilight… I am no princess with nopony to rule.”

Shepard nodded. “And please call me John. Shall we go?”

Twilight nodded and jumped off her throne. “Lead the way…”

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Author's Note

Willing to accept ideas as suggestions for future chapters. Post ideas below. All comments and feedback are welcome.