My Little Pony: Friendship Is Magic/Fanfic Recs/Crossover

Go back to the show's main fanfic recommendation page here.

Ace Combat: The Equestrian War by Valsion
 * Recommended by Silverstein222
 * Synopsis: The Griffin Kingdom prepares an invasion on Equestria and when the Wonderbolts become incapacitated by two griffin aces, a group of pegasus ponies, assembled by Firefly, becomes the land's main aerial defense force, supporting each other in the hardest of times. It's a story of revenge, friendship, sadness, struggles and sacrifices, a war which will change the lives of many a pony and griffon...

Better Living Through Science and Ponies by Pen Stroke
 * Recommended by Bailoroc
 * Synopsis: GLaDOS is free of Chell, free to continue testing, when she discovers a portal gun Wheatley tried to repair with duct tape. When the portal gun catastrophically fails, the enrichment center, GLaDOS, and Chell are literally dropped in the middle of Equestria. The mute test subject soon finds the world of ponies far more welcoming than the human world. But GLaDOS sees possibilities. Let the testing begin... for science.

Binky Pie by Miyajima
 * Recommended by Andyroid
 * Synopsis: Pinkie Pie is minding Sugar Cube Corner, when an unusual visitor from another world shows up and asks after her late grandfather, leading to Pinkie learning quite a bit more than she ever realized about him... and about herself.

Creeping Darkness by Pen Stroke
 * Recommended by Toko WH
 * Synopsis: ''There is a shadow to all of existence, a place that all worlds are shielded from by a thin veil. A Dark Place, where a single presence plots and struggles to consume all creation with its darkness. The author Alan Wake is one who has defeated this Dark Presence, but to save his wife and his world Alan had to remain trapped in the darkness.
 * Now, through his struggles to return to his wife, Alan has unintentionally released the Darkness and an old villain upon Equestria. To fix the mistake, Alan starts a new story with Twilight Sparkle as the protagonist. Can the unicorn find the strength to face the darkness, or is all of Equestria doomed to be the victim in the dreadful horror story?''

Deus Ex: Equine Revolution by Melon Hunter
 * Recommended by Valikdu
 * Synopsis: "The world is in flux; new ideals, groups and technologies permeate every level of society in this age of discovery. The field of augmentation has allowed ponies to improve themselves in ways that were unthinkable a generation ago. Yet, for every benefit, there is an inverse. A griffon civil war rages on the borders, feeding the profits of mercenary companies. Rising populations have forced the rich and poor ever further apart. Harmony is dying.
 * Mortally wounded after a fatal attack on her laboratory, an earth pony researcher is augmented against her will and sent out into a chaotic world in search of answers. But as her quest unravels this chain of events, she discovers an ancient conspiracy that will shake Equestria to its very core."

Doctor Whooves Episode 3: Atmos-Fear By Hephestus
 * Recommended by bigflatwhat
 * Synopsis: One week after the Changeling invasion of Canterlot, Twilight is taking a much needed vacation when she is met by none other than The Doctor, back from a lengthy trip to Equestria's past. Unfortunately for them a dark force has secretly taken control the Canterlot News Agency and is using its influence to spread paranoia and fear to the capital city. Now it's up to Spike, Twilight Sparkle, and The Doctor to find out who or what is behind this attack and stop them before it's too late!

The Dresden Fillies by Psychicscubadiver
 * Recommended by 7grayjay7
 * Synopsis: While traveling through the Nevernever, Harry Dresden finds himself chased by a pack of monsters and, after a blind jump between dimensions, winds up in Equestria. After the initial fish out of water comedy, the story gets more serious — as it turns out, even a Sugar Bowl like Equestria may sometimes need the skills of one such as Harry.

The Elements of Harmony and the Savior of Worlds by RK_Striker_JK_5 (alternate link)
 * Recommended by Schizo Technician
 * Synopsis: "An old legend from Dream Valley returns to Equestria, but is there a place for her in this new land? Crossover between G1 and FiM."
 * Note: Also appears on the Space Battles forums under the name "She Returns".
 * Now has a page.

Fallout Equestria By Kkat
 * Recommended by Kyman102, Erthilo
 * Synopsis: War. War never changes. Fallout: Equestria follows the story of Littlepip, a dweller of Stable Two who works as the apprentice to its PipBuck Technician. However, this changes when Velvet Remedy, a singer who is famous throughout the Stable, comes to her to get the padding on her Pip Buck repaired, but then disappears the next morning, having left the Stable afterwards, and Littlepip having removed her PipBuck. Now a target of scorn throughout the Stable, Littlepip is stressed beyond belief until she finds an override code inside of Velvet Remedy's PipBuck, which allowed her to escape the Stable. Using this code, Littlepip leaves the Stable herself to brave the dangers and horrors of the post-apocalyptic Equestrian wasteland.

Doctor Whooves Episode 2: Mines of Dragon Mountain. By Hephestus
 * Recommended by S Noble Jr
 * Synopsis: The sequel to Time Lords And Terror. After many adventures with the Doctor, Twilight and her friends find themselves back in Ponyville. With their lives beginning to show some semblance of normalcy the ponies are soon paid an unexpected visit from Zeitgeist Stardust, a multi-practice tycoon introduced in Time Lords and Terror. A series of events result in the ponies (and Spike) being taken to a much renowned luxury resort. However, all is not well in Dragon Valley as a mysterious race of creatures known as the Grundels sow havoc and mayhem throughout Zeitgeist's mines, fearing that his digging will unleash an ancient evil. Can the Doctor and company put an end to the bloodshed and stop the awakening of the demon god?

MLPFIM Fan Fic by Eq Am Rd (Fan Vid)
 * Recommended by Chabal 2
 * Synopsis: A thousand years before season one begins, Luna and Celestia's conflict escalates into open warfare. In this case, with B-52s and the memetically famous Orbital Friendship Cannon. Short but awesome.

My(stara's) Little Ponies: Friendship is Adventuring by John Biles (Alternate link, to a less complete text-only version, here)
 * Reccomended by Deek
 * Synopsis: Follow the adventures of Marcus (formerly Erik of Nort, a down on his luck adventurer) as he encounters the Elements of Harmony, an officially registered Adventuring Party in Equestria, the Republic of Darokin, Sind, the Five Shires, Alfheim, and Karameikos. A seamless integration of Equestria into the world of Mystara.

My Little Pony: Chaos in Equestria
 * Recommended by Forged in Darkness
 * Synopsis Chaos enters Equestria and corrupts countless ponies, leading to a massive civil war between Princess loyalists and Chaos worshipers.

Pony Space by OceanLord
 * Recommended by Troper541
 * Synopsis: Twilight accidently summons the engineer, and Necromorph slayer, Isaac Clarke into Equestria. Now she and Luna must deal with the armored interloper while they all search for the ponies who seek to ressurect the Marker. Rated M for gore and language.
 * Now has it's own page.

The Silent Ponyville Chronicles by Jake Heritagu
 * Recommended by Ace 2401
 * Synopsis: In an effort to end her recurring nightmares, Pinkie Pie enters her own mind with the help of one of Twilight's spells. Can she uncover the secret behind her nightmares and put the spring back in her step, or will she succumb to the twisted Otherworld that is her psyche?
 * Silent Ponyville 2, a sequel to the original from the same author, is now available on the same page. This time, Fluttershy and her friends has to enter her mind to find the truth behind the nightmares tormenting her.
 * Pairings: Fluttershy/Rainbow Dash in Silent Ponyville 2.
 * It has sense evolved into it's own fan universe, with various stories set in Alternate Universes. One of the better ones is Blood Chronicles, the story of how Twilight managed to get herself into the mysterious realm...along with a Serial Killer Killer and Deadly Doctor. Hilarity ensures.

Doctor Whooves Episode 1: Time Lords and Terror by Hephestus
 * Recommended by Andyroid
 * Synopsis: Another Doctor Who/MLP crossover. They must be fun to write or something. Equestria experiences a series of strange events, culminating with an eccentric brown stallion literally falling out of the sky. In her bid to get answers, Twilight embroils herself and her friends in an ancient war between two powerful races, one that may well destroy the multiverse.
 * Here's a hint: It's NOT the Time Lords and the Daleks, you've likely never heard of one of these races.

The Thessalonica Legacy by Dashukta
 * Recommended by S Noble Jr
 * Synopsis: In the 31st Century, humankind has spread to thousands of planets in the Inner Sphere. Once united under the glorious banner of the Star League, the Successor States and their noble houses now fight bitter wars over the scraps of empire. When a JumpShip carrying a special task force from the Federated Suns suffers a catastrophic misjump, the occupants find themselves stranded above a strange, beautiful world at once alien and eerily familiar. Meanwhile, in the peaceful realm of Equestria, Ponyville’s resident bookworm, Twilight Sparkle, has stumbled upon hints of a secret buried for centuries. A secret that may lay bare long-forgotten aspects of Pony history and culture. Our story begins on the planet Valexa, where the beleaguered Militia has launched a last-ditch effort to call for help against overwhelming odds.

Total Magic Pony Island by Tailslover13
 * Recommended by Chargin Chuck
 * Synopsis: Discord is once again loose, but after using his randomness to find some interesting information on some strange phenomenon in another world that has to do with an island and a bunch of humiliating events, the crazy spirit of disharmony and chaos comes up with a new, sick, twisted, disturbing plan that involves capturing 20 of the most popular ponies (and three non-ponies) and forcing them to play a new game while the rest of Equestria watches in horror (or most likely secret amusement and possibly envy of not being picked themselves). What does the rotten host Discord have in mind for our 20 unfortunate selections? Well, looks like you'll have to wait and find out! Maybe, just maybe, if Discord is feeling generous, the winner of his new "game" will get a grand prize. Everyone pick a character to root for and let's get it on!

Turnabout Storm by PWaaMLPfim
 * Recommended by Kytseo
 * Synopsis: The story goes that Rainbow Dash, the best flier in Equestra, was accused of murdering one of her competition in an upcoming race called the Equestria 500 (with the punishment being that she's banished to either the moon or the sun if found guilty). Her friend (and protagonist of FiM) Twilight Sparkle summons the best defense attorney in the universe (accidentally, initially wanting to summon the best in Equestria), said attorney happens to be Phoenix Wright. All that said, Nick attempts to adjust to temporarily living in Equestria while searching for the truth behind that murder (with Twilight as his resident Maya stand-in).
 * Comments: Judging from the first of the four planned episodes, it looks to be shaping up to be a pretty good crossover. From first impressions, I highly recommend it to Ace Attorney fans, bronies\pegasisters, and everyone inbetween.

World of Ponycraft by Cap'n Chryssalid
 * Recommended by Salvls and Whitebeardyamamoto.
 * Type: Crossover- Complete.
 * Synopsis: What could be more awesome than WOW?. Why, ponies of course. A recent finished work that tell the journey of the Mane cast to a new, exciting (and absurdly dangerous) world when the awakening of Deathwhing brakes the seal separating Azeroth from Equestria. Be warned: This is not a crossover with Word of Warcraft the work, this is a crossover between World Of Warcraft the MMORPG... yeah, just like it sound.

...And I was having such a nice day by Preda
 * Recommended by Preda
 * Synopsis: Doctor Who crossover fic. During an otherwise normal day of exploring the Ponyverse, the Doctor (recently turned into a pony himself) returns to find Discord playing around inside the TARDIS. You can guess what happens next.
 * Written pretty much so that Discord and the Doctor can meet, interact and out-xanatos each other, it seems, but features solid ideas and a few wicked twists.

Apple Bloom by NoRatCat
 * Recommended by Andyroid
 * Synopsis: Little Apple Bloom has been feeling neglected and unappreciated at home as of late. Yet one day she discovers a door leading to a fantastic world, but it isn't all what it seems.

Banishment Decree by Chuckfinley
 * Recommended by Dr Slide
 * Synopsis: Gilda is a top-notch spy who suddenly finds herself banished from her clan. Cut off from her intelligence connections and financial resources, she teams up with Trixie and Rainbow Dash to find a new line of work and figure out how she got into this mess.

Bridled Fury by Toon Ninja
 * Recommended by Andyroid
 * Synopsis: Kratos, Ghost of Sparta, finds himself taken to a world very different from his own. Will he be able to continue his journey for vengeance, or will the former god of war finally meet his match in Equestria?

The Wizard and the Lonely Princess by Harry Leferts
 * Recommended by Salnax 1
 * Synopsis: Harry Potter was a lonely boy who one day wished for a friend. Luna, trapped on the moon, wished for the same. And so their wishes are granted. How will the two deal with each other? And what about Nightmare Moon?

Canterlot Follies by Lady Moondancer
 * Recommended by Erik S
 * Synopsis: Less than brilliant gentlecolt Birdy Rooster is ordered by some of his dreadful aunts to do two things in Canterlot: restore his cousin Blueblood in the eyes of Princess Celestia after an horrible incident with some seamstress at the Royal Gala, and steal the Border Blanket from the Royal Museum for Uncle Pom's collection, to allow him to triumph over his rival Sir Catkin Basket. Birdy being Birdy of course gets into even more trouble. Luckily, he has his valet Greaves there to save him...

Disgaea: Disharmony of Friendship
 * Recommended by Kytseo
 * Synopsis: A crossover between MLP and Disgaea, Disgaea: Disharmony of Friendship starts Twilight as the typical Disgaea protagonist, a Chaotic Neutral (though claims to be evil) Anti-Hero of a demon who goes on a journey that starts off as a path of villainy, but eventually turns her good by the end Laharl and Mao (though she'll inevitably nullify her Character Development for the sake of lols in cameos, but I digress)]. The typical Trollestia interpretation for Princess Celestia (now Overlord Celestia) being properly altered and made into that of a kind and generous ruler. That said, Twilight doesn't approve, and journeys with her growing party in order to create their own alicorn superweapon they can use to dethrone Celestia and rule the netherworld in secret. All that said, hilarity ensues.

Mine, Little Pony!: Crafting is Magic by I'm Only Kidding
 * Recommended by: Mooncalf
 * Synopsis: A group teleportation spell gone awry strands the Mane six and Derpy in the Minecraft universe. Now, the heroines must find ways to survive, understand the bizarre physics of their new home, and build awesome, luxurious mansions and vanity projects. Surprisingly less silly than it sounds.

My Little Test Subject by Klutzybear
 * Recommended by: Ldude 893
 * Synopsis: GLaDOS finds a quirky, fun-loving, talking pink pony in the Aperture Science facility and puts her through various test chambers. Hilarity Ensues.
 * Pairing(s): none

Friendship is Magic Damnation is Alchemy by Anonymous Card Captor
 * Recommended by Forkinyoureye
 * Synopsis: A crossover between My Little Pony-Friendship is Magic and Fullmetal Alchemist. A former state alchemist looking to undo the past may have inadvertently lost his future when he come in possession of what he thinks is a chimera. Warning: OC-centric
 * Pairing(s): Fluttershy/Male OC, but it's more of a dramatic tool than shipping.

My Little Chrono: Triggers Are Magic Pav Feira
 * Recommended by Tropers/Salnax1
 * Synopsis: A Fusion Fic that places Friendship is Magic characters in the story of Chrono Trigger.

My Little Hangover by Mousetrap
 * Recommended by Chargin Chuck
 * Synopsis: It's Twilight Sparkle's 18th birthday, and in time-honored pony tradition her friends have dragged her to Las Haygas, the world-renowned City of Lights. They promise to give her a night she'll never forget. And with the lights, the glamor, and a few shots of Liquid Rainboom, it seems they're poised to deliver just that. But when Twilight wakes up to a destroyed hotel room, a hangover so painful it leaves her unable to do magic, a missing pony, and a slew of unanswered questions, she is forced to wonder: did they party too hard? Now, the five ponies must clean up their mess by piecing together a night that none of them can remember, all the while searching for a friend that could already be halfway across the desert... It's a lesson they'll have to learn the hard way: Some ponies just can't handle Haygas.

My Little Metro by RedSquirrel456
 * Recommended by Mad Cormorant
 * Synopsis: After the Apocalypse, the Stalliongrad Metro shelters what remains of ponydom from the mutant, radiation-infested wastes of the surface world. Lockbox, born in the Metro, has always been a rather private pony who liked to collect things, particularly things that remind him of the time before. When his home station comes under threat, a promise spurs him onto a quest to preserve the ramshackle remains of pony civilization, but can he find a reason to save what remains amid the violence, corruption, and depravity of the Metro?

My Little Pony: The Neigh of Cthulhu by CoreyW Seriously epic, great characterisation even the great Trixie.
 * Recommended by capeclare
 * Synopsis: Friendship is Magic meets H.P. Lovecraft. The Great and Powerful Trixie stumbles upon the Necronomicon. Now the dead are walking and the city R'lyeh is rising. Can Trixie and all of Ponyville defend against nameless horrors from beyond their world?

Of the Time Before by Clockworkchaos
 * Recommended by Exploding Frogs
 * Synopsis: A crossover with Exalted, told in the style of the Legend of the Titans from the Ink Monkeys articles. No one from Exalted is directly named, but it's very clear who is who if you're familiar with the series. Of the creation of the Divine sisters and their peers, and of Equestria and of the Elements of Harmony.
 * Pairing(s): Luna/OC is hinted at, but never confirmed.

Order From Chaos by Twilight Snarkle
 * Recommended by Ace Of Scarabs
 * Synopsis: Dr. Ivo Robotnik, utterly tired of his constant battles with Sonic, decides to just give up and live out the rest of his life in a retirement of quiet solitude. When he finds himself in Equestria... Well, spoilers abound.
 * Yes, I know, it's a Sonic crossover, but it truly is a beautiful story. It's more of a villain-redemption story, and isn't at all what you would expect.

Ponies One Half by Emma Iveli
 * Recommended by Dr Tempo
 * Synopsis: From FF.Net: "Thanks to a teleportation accident, Twilight and her friends are stuck in another universe, not only that but the first thing that happens to them is that they get cursed. And that's least weird thing that happens to them." This is only the second ever FiM/Ranma crossover; the plot may be basic, but For Want of a Nail, among other things, kicks in from the start.
 * Note: Now has a "director's cut" version in FIMFiction.Net here.
 * Also has a page here.

Poisoned Sugar by LordOfTheWrongs
 * Recommended by Sanwire, S Noble Jr
 * Synopsis: A Doctor Who crossover fic. The Doctor is understandably upset when he mistakenly lands in Equestria, but he quickly realizes it isn't chance that brought him there. The universe is wounded, and Nightmare Moon was only the tip of the iceberg.

The Rummy Business of Old Blooey by Cloud Wander
 * Recommended by Jakes Brain
 * Synopsis: From Equestria Daily: "If you will permit me, sir: on the eve of the Grand Galloping Gala, one of Mr. Barney Trotter's acquaintances has become entangled in a most ill-advised romantic situation. To extricate himself from this unfortunate predicament, this friend has sought out Mr. Trotter's invaluable assistance, and even accepted some small suggestions from Mr. Trotter's valet, Cheese. Given the delicacy of the matter, it is feared that, if all precautionary steps are not carefully taken, a farce may ensue." In other words: My Little Pony meets (a very thinly disguised) Jeeves and Wooster.

Sailor Ponies by Emma Iveli
 * Recommended by Dr Tempo
 * Synopsis: From FF.Net: "FiM AU. An evil force from 1,000 years ago has returned, Princess Luna has Twilight and the others become a new force of justice, the Sailor Guardians! With the powers of the planets of their side they be able to defeat this evil?" Has Emma's trademark humor, while throwing in some surprises along the way!

A Stranger in Ponyville by Brony Fife
 * Recommended by pickadish
 * Synopsis: A crossover with notorious Internet lolcow Chris-Chan, as written in the style of H. G. Wells... at least, at first. Basically, the situation becomes more and more surreal until the very fate of Ponyville hangs in the balance...

A Study In Rainbows (b/w The Hound of Ponyville) by Thanqol
 * Recommended by Joanassie
 * Synopsis: Returning from Zebrica, Rainbow Dash finds her lot cast in with the brilliant and eccentric detective Rarity, as they unravel a crime most foul. Starring Rainbow Dash as Watson, Rarity as Holmes and Fluttershy as Lestrade.

Sweetie's Mansion by Moon Shooter
 * Recommended by King Sonn Dee Doo
 * Synopsis: (from FIM Fiction): "When a mansion appears out of nowhere in the outskirts of town, The Mane 6 are all invited to a housewarming by Specter Yield, the owner of the strange mansion. Hours after they leave to attend the party, the Cutie Mark Crusaders find themselves in this mansion. Eventually, Sweetie Belle finds herself alone in this massive mansion, trying to save her friends, and discovering the truth behind this haunted mansion. Will she be able to rescue her friends... and possibly all of Equestria from the ghostly presence?

Tales of Harmony by Starwind Dood
 * Recommended by Tropers/Kytseo
 * Synopsis: (from Equestria Daily) Fan-fiction that will show you the harmony found in our hearts!

The fate of Equestria will be decided not by the madness of battle, but by the harmony between each other...

Twilight, a student from Canterlot, and her dragon companion, Spike, find themselves caught in a mission to find the elements of harmony to stop the the crazed mare, Nightmare Moon. Equestria is not a land of love and tolerance, but a land that has been ravaged by racial conflict, sudden earthquakes, and the shadows within a pony's heart. Only with friends can Twilight find the strength to stop Nightmare Moon.

To save Equestria, Twilight will have to prevail against power-hungry ponies and those who would wish to stop the gathering of the elements of harmony. Honesty, Laughter, Kindness, Generosity, Loyalty, and Magic. Are these strong enough to fight the wicked?

Not the Afterlife I Signed Up For by inoeitall
 * Recommended by Dynamic Dragon
 * Synopsis: Usually when you are killed, you die. Of course there are exceptions to every rule. Usually those exceptions don't end up in a world full of colorful talking ponies with 3 other people from random points of Earth's history, but hey, I can't complain too much. Now if we can just figure out what happened, how we ended up in Equestria, and who is responsible for this mix up...
 * Comments: A hilarious "humans in Equestria" fic, with witty narration and a strong sense of mystery.

The Three Hooves by Paleo Prints
 * Recommended by Kytseo
 * Synopsis: 'John Smith' has settled in Ponyville with his wife and two daughters for many peaceful years. When the TARDIS gets a temporal distress call, Doctor Whooves and his family find themselves lost in time. Now Derpy must contend with not only monsters and maniacs, but future and past versions of her own husband!

Waking Nightmares by Jonathan "KnightMysterio" Spires
 * Recommended by Conchshellthegeek 7
 * Synopsis: "Luna's nightmares herald the arrival of nine warriors from another world, who have unwillingly been turned into ponies by the force that brought them there. Why were they transported to Equestria? And what is the horror that haunts Princess Celestia?"
 * Can also be found here.

Friendship is the Key by appendingfic
 * Recommended by Animenutcase
 * Synopsis: "When dark clouds gather over Equestria, it's up to Twilight Sparkle and her friends to explore other worlds, face tests of their virtue, and save everypony from darkness."

My Little Phinny: Ferbship is Magic by Bpendragon
 * Recommended by Cabbit Girl Emi
 * Synopsis: "A crossover between Phineas and Ferb and My Little Pony: Friendship is Magic, The boys build a portal to Equestria and adventures occur in both worlds."

The Dresden Fillies by psychicscubadiver
 * Reccomended by omegaman
 * Synopsis: Narrowly escaping from the Nevernever to a realm that does not involve getting eaten by a hundred demon monkeys, Harry Dresden finds himself in a cutesy Sugar Bowl that is is rife with environmental magic. He reacts to the situation about as much as you can expect (namely, by actively suppressing the urge to pick up the adorable locals and squeeze them like some manic five-year old girl). And the local population is not exactly sure what to make of this giant, bipedal creature that claims to be from another world, and by any accounts, is probably one of the most dangerous creatures they'll ever meet.
 * Now has a sequel.

12 by Squeak
 * Recommended by Whome 1
 * Synopsis: A mysterious blue box suddenly crashes into Twilight's library, causing much uproar in Ponyville. From this strange box comes an eccentric brown stallion sporting an hour-glass cutie mark and a sharp wit. However, following the introduction of My Little Timelord it is made apparent that he was not alone in his discovery of Equestria as three ominous statues descend from on high. Soon Twilight, Pinkie, Spike, and The Doctor find themselves battling these denizens of the Abstract Plane for the future of Equestria and, quite possibly, the entire MLP universe!
 * Has two alternate universe sequels: First is his own work, Traveler, which is about the Doctor and Twilight going to a dark, depressing future, and other is the Audio Drama series Doctor Whooves Adventures, which is headed by him. As of this writing, the two are not intersecting, and are not in continuity with one another. Check out Doctor Whooves Adventures at Pony In A Box Production's blog, here, or at their trope page.

Ed, Edd, 'n Pony by Cannox
 * Recommended by Nightelf 37
 * Synopsis: After a spell gone awry, Twilight Sparkle comes face to face with three very special people: the Eds! What fate befalls our three Eds in Equestria, and can the Elements of Harmony possibly cope with the Masters of Discord themselves?
 * Note: Judging by the publish date, it seems to take place before Season 2 of Friendship Is Magic, so the author probably didn't mean any reference to the villain Discord.

Substitute Harmony by Blayze Kohime
 * Recommended by 45xxx
 * Synopsis: When strange ponies from another world suddenly pony-nap all her friends, Pinkie Pie must find a way to defeat their master all on her own. Blamed for the crime herself, she has no help from Celestia and just about every pony in Ponyville is convinced that she's finally cracked. Who can she possibly find to fill in for the other elements to defeat the ancient evil behind it all?

Name's Ellis by MAGO5
 * Recommended by Poptard
 * Synopsis: Applejack finds a strange visitor in her apple orchard one day, with even stranger stories to tell.

Rorschach in Equestria by Ex-Nihilos
 * Recommended by Nightelf 37
 * Synopsis: Instead of being killed in the cold Antarctic by Dr. Manhattan, Rorschach finds himself rematerialized in a strange new, pony-filled world. He finds himself drawn into the lives of the ponies of Ponyville but some ponies fear that this sociopath will bring danger and darkness to an otherwise peaceful existence. Will the mane 6 help Walter Kovac find peace within himself, or will he bring them all down with him in his cold views of reality and existence?

Lyra's Pyro Predicament by Darrtaa
 * Recommended by Nightelf 37
 * Synopsis: When a mishap causes two para-dimensional weapons to collide with one another, RED Team's Pyro is sent flying from the Team Fortress 2 universe into the alternate universe of My Little Pony, where he is almost instantly discovered by Lyra, who shelters him in her home.

Having him hidden in her small townhouse isn't easy; keeping him from setting things on fire, teaching him that not every cart that passes by is cause for alarm, and that blue ponies are not something to be suspicious of.

However, with Nightmare Night soon approaching, Princess Luna feels that there may be something more sinister riding on the coat tails of Pyro's grand entrance; the first human to ever set foot in Equestria some thousand years ago...

My Little Naruto: Friendship is--WHERE AM I!!? by DragonLS
 * Recommended by Nightelf 37
 * Synopsis: Naruto's life has been taken, and is given a second chance at life due to certain circumstances... However, what he didn't realize, is that he would be living in a world of ponies and magic, not in his own world. Will Naruto learn to put his past life behind, and accept his new life? Or will he go insane, stab himself in the head, squat down sucking his thumb, and yelling for his mommy? Let's find out!
 * Notes: Takes place post-Time Skip, but before his meeting up with Sai. Gets slow in the beginning, but comes up to speed in the second chapter.

Super Equestria by PonyofTacos
 * Recommended by Nightelf 37
 * Synopsis: Samus Aran is on the run. The Federation has branded her a traitor. Now with only her gunship and recently acquired abilities, she must escape. Her escape lead her to crash land in Equestria. Unknowingly she will disrupt all life of everypony there. Focuses on Samus (of course), the Mane Six, and Lyra.

The Stars, the Seal, and the Kraken by CLAVDIVS CAESAR
 * Recommended by Nightelf 37
 * Synopsis: An ancient evil escapes from its prison... A familiar story for the bearers of the Elements of Harmony, but against a threat even older and more alien than Discord, victory will be no simple thing. Even so, with friends rallying to their aid and a former rival fighting by their side, in this strange aeon even death may die.

Mario & Luigi: Of Ponies and Plumbers by EverSoNitro
 * Recommended by Nightelf 37
 * Synopsis: Princess Peach Toadstool of the Mushroom Kingdom has come to Equestria on important diplomatic business, bringing with her the superstars of the Mushroom Kingdom, Mario and Luigi. But, when Discord is released, and aids Bowser's forces in invading Equestria and kidnapping Peach, Celestia, and Luna, Twilight and her friends must work together with Mario and Luigi on an adventure spanning two kingdoms, to rescue the princesses, defeat Bowser and Discord, and return Equestria and the Mushroom Kingdom to their former glory.

Doctor Whooves and the Other Doctor by hasbrohoof
 * Recommended by Nightelf 37
 * Synopsis: Not your typical Doctor Whooves fanfic. A series of events cause the TARDIS to blast into a dimension populated by ponies and crashes. While waiting for the TARDIS to repair itself, The Doctor runs across a certain brown stallion, whom he will discover is a reflection of himself in more ways than one. But even after The Doctor was gone, his mere presence created a ripple that would awaken an ancient being. Continued in the sequel Doctor Whooves and the Sea of Dreams.

Whip and Wing by Fernin
 * Recommended by Eegah
 * Synopsis: Daring Do's latest race for an artifact against Ahuizotl results in her meeting her match from another universe: Indiana Jones.
 * Now with its own page

Zim Invades Equestria by Steeve Lee II
 * Recommended by G0vnah
 * Synopsis: What will happen when everyone's least favorite Invader stumbles into the world of My Little Pony: Friendship is Magic? Horrible things. Horribly funny things. It's only a plot outline, but might as well be a fanfic, with how it reads. It does switch tense occasionally, but aside from that it's not a bad fic outline. Worth a read.

PROTOTYPE Equestria by Azzazel
 * Recommended by User:Nightelf 37
 * Synopsis: Takes place after the events of the video game Prototype. The infected have started to die out and the military have begun to move out in spite of still hunting Alex Mercer. Alex received a call from Dr. Ragland, who said that his sister Dana has awoken from her coma, and that he's received interesting information; a group of Blackwatch scientists were working on a new weapon with cold fusion to be used on Alex, should it malfunction, it could wipe out the entire city.

Alex headed for the site where the weapon was and infiltrated the base. He's soon found out and gets into a fight. In the midst of that, a black vortex formed in the area, sucking in everything, including Alex himself. Of course, we all know where he's ended up.

Spike 10 by MasterZero
 * Recommended by Nightelf 37
 * Synopsis: Spike is walking through the Everfree Forest when a strange metal sphere falls from the sky. Inside, he finds a black and white watch, which latches onto his left arm. Now, he can't get it off, but on the bright side, he now has the power to turn into ten different aliens. He's become Spike 10, the Hero of Ponyville.

Left 4 Derpy by Edmar Fecler
 * Recommended by Nightelf 37
 * Synopsis: After a long day of work, Ditzy (Derpy) Doo wakes in the night to find that she is in the middle of the zombie apocalypse. Worst of all, the zombies arent even ponies! Instead, they are some strange type of two-legged creatures with hands. fortunately for her, she is found by four of these creatures that dont seem infected. But can they help her escpae this nightmare? For that matter, can any of them escape the hell-hole of a city they find themselves in?

Friendship is Aura by KangTheSpartan
 * Recommended by Nightelf 37
 * Synopsis: In the aftermath of a huge explosion in the Everfree Forest, Ponyville soon finds itself as the new home for Lucario, an "Aura Pokémon" from another dimension. While he avoids explaining what has happened to him and where he came from, he repays his new friends' kindness by protecting them from the evil forces that suddenly appears around Equestria. All the while, a certain princess of the night watches his every move, unable to judge if this new visitor will bring safety or utter destruction upon the land.

Discord In Gotham by Jabberspike
 * Recommended by Nightelf 37
 * Synopsis: Thanks to a certain imp from the fifth dimension, Discord has come to Gotham City intending to prove he's the best there is at spreading chaos. Now the Joker has to stop the draconequus from taking his job as Gotham's chief chaos-causing clown.

The Shogun Six by Warwolf
 * Recommended by Rider
 * Synopsis: Taken from the Website: "AU. Dusk Shine is the apprentice to the Shogun of Equestria. When an ancient evil threatens to return, Dusk must gather the only thing that can stop it: The Elements of Bushido. Now Dusk begins a quest that will bring him together with five other ponies. Their journey will bond them together as brothers in arms for the rest of their lives. Their adventures will make them ... the stuff of legends.... First in a Saga."
 * Comments: A fanfic that takes place in an Equestria with a hyper modern (and in some cases futuristic) amount of tech where ponies can switch between a normal pony form and an anthro form. Equestria is a shogunate ruled, as the name implies, by a Shogun, a male version of Luna called Lunaris. His ward Dusk Shine must unite a group of ponies who will come to be called the Elements of Bushido to stop an oncoming evil. Humans, though not yet seen, exist in this world as well due to an event called "The Great Merger". The central protagonist, Dusk Shine, and his compatriots all appear to be trained in the martial arts and have thus far, been referred to as young Samurai or as Samurai in training. Appears to be an outright strange take on the pilot episode in some respects. The fic is currently on-going. So far three AU counterparts of the girls have been seen: Dusk Shine, Flash, and Ash Jade. (Counterparts to Twilight, Rarity, and Applejack, respectively, though according to Word of God, they are not necessarily genderflipped versions of the characters, but rather different ponies living lives that the Mane Six might have lived in different circumstances) Ash seems to break the currently established rules of the world the fic takes place in due to the fact that  However, this might fall in line with the tech that seems to exist in the world of the fic.
 * Tags: Crossover (though he hasn't said with what yet.), Dark, AU, Human, Adventure

Iron Will's Swim Seminar by Kanashii Panda
 * Recommended by Gilgamesh
 * Synopsis: A brief animated Fan Film of Iron Will doing the dance from the closing credits sequence of Free, for a seminar on swimming.