Shortly before his assault on the Collector Base, Commander Shepard is tasked by The Illusive Man to investigate the disappearance of a Cerberus science team who had gone to investigate the origin point of an extremely powerful weapon which had been used against the Reapers 36 million years in the past. Upon following their lead to a system outside of Citadel Space, the Normandy is attacked by automated defenses that separate Shepard and his away team from the Normandy.After making planetfall and taking cover in an underground facility, Shepard is attacked by robotic tendrils which pull him away from his companions. When he awakens, Shepard finds that he has been transported to the colorful and magical realm of Equestria, and in the process has been transformed into a pony.After getting to know a bit about this strange land and some of its more illustrious inhabitants, however, Shepard soon finds that he is far from the only thing that isn't what he seems to be. The entire world of Equestria is a virtual reality simulation that has been running for millions of years, and the Equestrians he meets are the descendants of the ancient race of Equines who built the facility. As Shepard tries to return to reality, his choices and actions will determine the fate of an entire species who have never known anything about the world outside their simulation.This is the beginning of Mass Effect 2 DLC: The Equestrian Equation by Loyal2Luna (author of Doctor Whooves The Series). The Equestrian Equation is notable for not only bringing the residents of Ponyville into the Mass Effect universe in a manner that operates within the logic of the video games, but also allowed readers to cast their votes on Shepard's actions at the end of each chapter, with the story adjusting to fit the results.Has a sequel called Shades of Twilight focusing on the trials of the Equestrian Herd after they are introduced to the larger galaxy. After being removed from the Equestria simulation, the Equestrians are refugees. With only a few hundred of their species left in the universe, it falls upon Madam President Twilight Sparkle to determine how they will create a place for themselves in the galactic community.Shades of Twilight is currently ongoing. Like The Equestrian Equation, readers are able to vote on the decisions that Twilight must make to build her society up from nearly nothing, as well as protecting them from unsavory elements who might try to harm the Herd. All while the imminent threat of Reaper invasion hangs over their heads.
"42, please access the Codex for examples pertaining to this series."
Aliens Speaking English: Justified because the ponies, in preparation for their eventual discovery, were conditioned in the system to speak at least one of the languages prevalent in the galaxy at any one time. Earth English was chosen specifically because Princess Luna became infatuated with human culture and the works of writers like Mark Twain, Isaac Asimov, and William Shakespeare.
All There in the Manual: Like the Mass Effect series, Loyal2Luna updates a blog that serves as the Codex for the Equestrians as new information is revealed in-story.
A.I. Is a Crapshoot: Averted by Luna and 42, borderline with Celestia, and fully embraced by Discord.
Arc Words: "Harmony for All," the philosophy of the ancient Equines.
Bedlam House: The appropriately-named Bedlam, a facility in Canterlot which is where problem cases or aliens brought into the Equestria simulation are sent to be brainwashed into being harmonious members of Equestrian society.
Beware the Nice Ones/Bullying a Dragon: The ancient Equines were friendly, cooperative, and believers in the Last-Second Chance. That said, they would deal swiftly with those who refused to take their one chance using overwhelming force. The Codex goes into more detail, describing the aftermath of the first recorded attack on an Equine colony by a rogue faction of the Griffar Imperium. The Equines militarily, economically, and politically annihilated all traces of this faction, then afterwards devoted resources to helping the newly-created Griffar Republic rebuild. This is also the only existing record of a direct attack on an Equine colony before the arrival of the Reapers.
As those who have made the mistake of trying to mess with Twilight discovered, this trope is very much still in effect.
Bittersweet Ending: Shepard saves the ponies with the help of the Mane Six, but Equestria and the sheltered, idyllic existence that everypony knew there are all gone forever. And now the ponies must try and survive in the much harsher world of the Mass Effect galaxy with only enough general knowledge to get by and the imminent return of the Reapers hanging over their heads like a shadow.
Big Damn Heroes: Twilight pulls this off when Dr. Milligan has an unarmed Shepard pinned down in the Harmony Core chamber.
Cassandra Truth: Pinkie Pie. The only one immune to the Equestria System's use of Laser-Guided Amnesia to preserve The Masquerade, any attempts by Pinkie to explain things to other ponies just gets wiped from their memories immediately afterward. Eventually she just gave up on trying, and decided to simply have fun with it instead.
Pinkie: (to Twilight) "I mean, do you have any idea what it's like to have something so important to tell everypony, something that their lives absolutely depend on… and have them just ignore you?"
Shepard: "Yes… I do."
Shepard trying to explain to Twilight that he's not a pony. She thinks he's insane...and then more and more evidence starts cropping up seemingly verifying his story.
Chekhov's Gun: Pony Shepard's Cutie Mark. Or to be more accurate, the fact that he doesn't have one, and neither does Dr. Hern before Celestia Mind Rapes her, but Milligan does. It turns out that Cutie Marks are actually tracking tags placed on ponies registered within the Equestria System, to allow the three AI overseers to keep tabs on them. The fact that Milligan had one was proof that he, in fact, was not able to resist the mental conditiong at Bedlam. Discord had merely modified that conditioning to suit his own ends.
Culture Clash: The main reason why District 1286, a.k.a. "New Ponyville", was granted to the Equestrian Herd was to mitigate this effect, both for the Equestrians who would otherwise be suddenly thrust into a completely alien community and for the settled aliens who would otherwise have to deal with the sudden influx of a refugee species. The media backlash that would have resulted from tossing the Equestrians into an occupied District probably wouldn't have helped, either.
Cuteness Proximity: Many species find the Equestrians to be absolutely adorable. Even Jack does; though being Jack, she expresses it through suspicion and hostility.
Ditzy Doo and many of the foals of the Herd suggested deliberately invoking this to encourage charitable donations that would fund New Ponyville's initial development, but the idea was turned down.
Deconstruction: In a roundabout way, this fic deconstructs many of the Fridge Logic elements of MLP:FIM by explaining them as products of Equestria being a computer simulation.
Downer Ending: A blog post by the author reveals that if the voters had chosen to upload the servers Discord would have escaped to the Normandy, killed everybody on board, and left to have his "fun" while everybody left in the system died.
Everypony Lives: Sort of. All the surviving ponies from the Equestria System manage to escape aboard the Normandy. Except for Granny Smith, who dies in the med-bay from unavoidable complications due to extreme old age.
End of an Age: At the end of Equestrian Equation, the ponies are awakened from the Equestria Simulation and must face the real world for the first time in millienia.
Fatal Flaw: For the Equines, their trusting and cooperative natures made Reaper Indoctrination especially devastating to their war effort.
Fluffy the Terrible: The Harmony Cannon. The beam it fires looks like a rainbow. During the Star Daemon War, it was used to kill Reapers.
Going Critical: The Harmony Core, after its control systems are damaged by gunfire.
Heroic Sacrifice: Doctor Hour Glass, in order to trick the Reapers into believing that everything of value in the star system had been destroyed. Luna refers to him as "the last being I would ever call a hero."
I Call It Vera: Lt. Pyres in Shades of Twilight calls his Viper sniper rifle "Freya".
In Medias Res: The Equestrian Equation begins with Shepard waking up in Equestria as a pony and then goes back to the crew of the Normandy receiving the mission to find Milligan's team from TIM.
Laser-Guided Amnesia: Used to keep the Equestrians from realizing that they are living in a VR simulation. Pinkie Pie happens to be immune, but was unable to share this knowledge for years since anypony she told would simply forget immediately afterward.
Last-Second Chance: A defining feature of the Equines' approach to diplomacy. Hostiles will be offered one chance to cease hostilities. Those who complied were offered friendship and the opportunity for mutual benefit. Those who didn't... probably ended upwishing they had.
Living Battery: Celestia's plan upon realizing that the Harmony Core was eventually going to fail. By altering the Equine species into the modern Equestrian species to maximize biotic potential, she intended to make the Equestria system self-sustaining by drawing upon the biotic power of its inhabitants.
Malicious Slander: The Herd find themselves the target of a "documentary" called The Cost of Grazing which paints them as genetically-engineered puppets of the Alliance, designed to somehow infiltrate and take over the Citadel for their human masters. And this isn't the first time that company has done this; they actually got off lightly compared to the Quarians.
Meaningless Villain Victory:Even if Milligan had been able to download the contents of Equestria's servers to TIM, Cerberus would still not have access to the Harmony Core, the key to nearly all advanced Equine technology, because the plans to build one were not on the server.
The Equestrian Royal Guard count too, in a way, as they are actually security programs with no individual personality of their own.
Medium Awareness: In-universe, Pinkie Pie is aware that her world is a digital simulation, which is what allows her to do crazy, physically impossible things.
Mega Corp.: Epona Systems Corporation was a rare benevolent version, also serving as the de facto governmental body of the Equine race. Though they acquired enough power and influence to become the dominant superpower of their cycle, their preferred method of doing so was through mediation with other species and technological innovation, rather than oppressive force.
Mind Rape: In order to preserve the Equestrian simulation, Celestia attempts to alter Patricia's mind to make her believe she's a pony. The process nearly lobotomizes her.
This sort of mental programing is routine for ponies who don't fit Celestia's ideal "harmonious" psychological profile. Fluttershy is revealed to have gone to an institute for being aggressive in her youth and was subjected to some kind of mental torture that turned her into an Extreme Doormat and caused her to repress her memories of the experience.
The same was attempted on Dr. Milligan, as he was labeled insane for thinking himself a human.
Noodle Implements: Pinkie Pie's plan to infiltrate the Canterlot Library involves the use of balloons, a wooden staff, a big straw hat, a record player, a dozen chocolate cupcakes, and a live squid.
Revealing Coverup: System AR-43281, where the Equestria facility is located, is at first glance home to nothing but some uninhabitable planets with absolutely nothing of interest or value. This trips EDI's logic filters because the odds of there being a star system that bland, with absolutely nothing of value, is so mathematically infinitesimal that either they have found the most impossibly generic chunks of rock in the galaxy, or their scanners are being fed false data.
Robot Buddy: 42 of 50, a Changeling drone who ends up becoming Twilight's personal assistant at the end of The Equestrian Equation. He is a fully sentient AI with the personality of Twilight's "Number One Assistant", Spike.
Galaxy of Fantasy is mentioned to be created by "Ionic Storm", a Captain Ersatz of the now-defunct Ion Storm of Deus Ex fame.
Spanner in the Works: Shepard, of course. Having the contents of the Prothean Cipher in his head made his brainwaves disruptive to the simulation.
Sudden Video-Game Moment: In order to help the others infiltrate the Canterlot Library, Pinkie uses her hacking prowess to convince the guard programs that they are fighting a turn-based RPG battle, complete with accompanying background music. One character even lampshades the Fridge Brilliance of this.
Take A Fourth Option: The voters (and by extension, Twilight) did so in deciding how to deal with the slanderous documentary, The Cost of Grazing. When offered the choices of either ignoring it, creating a public awareness vid of their own, or suing the production company, a reader going by "Silent-Judge" suggested contacting Emily Wong and opening New Ponyville up to full media access, which proved popular enough to win with nearly two-thirds of the total vote.
Tempting Fate: While talking about his role in New Ponyville, Lt. Pyres tells Twilight to just consider him window dressing unless something serious happens. A few minutes later, the two of them are told that a group of Krogan are loitering in New Ponyville and refuse to leave.
Two Scenes, One Dialogue: Happens when Princess Luna is explaining to Shepard various facts and details relevant to Equestria and the history of the Equines. At the same time, the members of his crew inside the Lunar Base in orbit are receiving similar information from a recording made by the long-dead Doctor Hour Glass.
Wham Episode: Arc 2 Part 3 of Shades. What starts as a routine filming of a documentary by Emily Wong escalates when New Ponyville is bombed as a distraction to kidnap some ponies, with Rainbow Dash badly injured while trying to stop the kidnappers.
What Might Have Been: This blog post by Loyal2Luna goes into detail about how The Equestrian Equation would have ended if readers had opted not to bring the Equestrians en masse out of the simulation.
What The Hell, Applejack?: In Shades Twilight gives a reaming to Applejack who kidnapped Dr. Hern from Huerta Memorial due to a confrontation with Hern's family at the hospital.