Future MLP stories part 4

More future stories. Boy, am I loving this!

The Second Unicorn and Pegasus War: Things goes wrong in Equestria as for some reason, the unicorns and Pegasi declare war on each other, forcing some of the Mane Six to take their own side. Unknown to everypony, the war was manipulated by some old enemies of theirs.
Villains: Twilight Moon, Rainbow Chaos, Chrysalis and the Changelings, Tirek

Spike's Birthday: It's Spike's birthday once more and Twilihght and his friends want to work hard to give the baby dragon the best party there is. Can they do it and avoid another huge and greedy dragon from last time?

The Apocalypse Countdown: The time where Smaug orders all of his members to begin their finale strike against Equestria, they have the army, they have the power, the time to strike & bring the downfall of goodness as struck the hour. But the Mane Six and their strong friends are ready for the challenge, they have seen how strong some of the separate members are, but that won’t frighten them. But of course, the challenge will be far greater, for the gang now truly are up against the third strongest evil force in Equestria (second being the Dark Mystics & the top number one being Grimmore). And even this time, even Trixie is now at the mercy to fight for the side of evil, but what happened is shroud in mystery? As the heroes go off in try and fix each of the problems the organization has done to their land, they shall learn terrible, evil, horrible things of each of the evil member of the Apocalypse Ponies & what their strength lies in; from Grimmore’s Copied Crystal holding a potion of the Triforce, to those being vessels to the Eight Demon Lords, and far worse, the complete structure of the Dark Mystics own: Elements Of Darkness. The Mane Six’s problems seem almost impossible, but from despair, comes a new light…the light of Element Evolution will finally be revealed towards those that are the Users to the Elements Of Harmony. And during the final confrontation against Smaug The Superior, will another surprise be in where Ben faces Shadow Ben (& Evil Version of himself) to beat to join the others, and bring forth another new unlock item: a mask of great power. Will the new powers for the heroes be enough to finally defeat Smaug & end his evil reign….
Villains: All the Apocalypse Ponies: Smaug, Suffocator Jill, Warring Malice (A bit before turning good), Starven Fran, Deadly Rager, Wilco, Twilight Moon, Fluttercruel, Crarity, Rainbow Chaos, Liarjack, Psycho Pie, Trix Lulamoon (Trixie’s Alicorn form & approximately under a spell after being found out as being a spy?), & Merluck.

Boris Finds Out (short story; happens JUST before "Trixie the Fugitive"): Boris finds out that Trixie is a spy for Princess Celestia and, more importantly, is increasingly afraid that Smaug might be on to her. How will he react to the discovery and will Trixie be able to convince him that her feelings for him are geniune?
Pairing: Boris x Trixie
Villain: Smaug

Trixie the Fugitive!: After getting tired of suffering punishment and abuse at the hands of her father and the Apocalypse Ponies, Trixie quickly quit and escape, taking Boris, Boxco and Dum-Dum with her and hiding out at Castle Canterlot. Smaug send the Apocalypse Ponies to get her back. Will the ponies defend one who is used to be their enemy? And will Warring Malice be forced to attack her only friend?
Villains: The Apocalypse Ponies

Helping a Earth Pony: Boris: Boris is now reformed and has no idea what he would do now, feeling worthless and powerless. Twilight decides to help her former pursuer in any way she can.
 
Empty Equestria: An unknown being known as the Entity arrives and begins turning Equestria into a wasteland, judging the place not suited for living due to the fact that it isn't a peaceful place no more. Will the ponies stop the Entity or will Equestria be no more?
Villain: The Entity

Ben and Boris's Adventure: Twilight and Trixie disappears and their boyfriends go out into the farthest reaches of Equestria to find them, especially when it comes to these two rivals. Will Ben and Boris finally end their feud to find their loves?
 
Han Zero: Dead Or Alive?: Han Zero went on an exploration to get rid of some weapons, but winds up being missing. While Han Zero is presumed dead by most, Luna, the Mane Six, the stallions, Spike and the fillies suspect that he's still alive and goes on a quest to find him.

Speedy Blue Blurs: (crossover with Looney Tunes) Rainbow finally did it. She broke through the universal barrier, sending her and Dr. Lizardo into another world, meeting up with the Road Runner. Of course, Dr. Lizardo teams up with Wile E. Coyote to track both speedsters done. Easier said than done!
Villains: Wile E. Coyote and Dr Lizardo

Earth Filth Ain't So Bad: Boris is getting used to being an Earth pony but still doesn't like them. But when he's been assigned to be in an activity for Earth ponies, the former villain realizes that maybe there's something about them that he now understands.

Bad Apples: Tough's side of the family came to visit and they are ill-tempered and mean as he is. Can Ponyville survive the Tough Apple family?

The Party has been Doubled: Pinkie and Brian decide to make one huge party for Ponyville. But when a misunderstanding occurs resulting in an argument between the two, can Twilight and her friends help resolve this conflict?

Nyx in Toyland: Nyx and her friends arrive at a toystore that just opened up in Ponyville. But when Royal Slash purposefully locks them in the store during closing time, Nyx must help her friends escape the store before their family gets worried!

My Mortal Pony: Takes place in the new MK timeline. Shao Kahn, restored back to life, decides to take on Equestria to get the Elements of Harmony. Raiden resurrect his dead friends to team up with Mane Six and their friends to stop the forces of Outworld.
Villains: Shang Tsung, Shao Khan, Baraka, Dr Lizardo, Wilco, Chrysalis and Tirak

Apple Birthday: It's Applejack's birthday and the ponies are working on turning it into one huge rodeo. Will it be a big success and without much trouble too?
 
Boris Versus Boris: Short story. To help Boris understand how he used to be, Celestia uses a spell to make him fight against his dark side. Will the former villain, now an Earth pony, be able to stop what he used to be?

Bringing back the Old Gen: The old Generation of Ponies from generations ago are restored back to life, ending up in the current timeline of Equestria. How will they live in this strange new world, a newer version of Ponyland that they once knew?
 
The Trifecta: Brought together by Dr. Lizardo, Twilight Moon, Psycho Pie and Rainbow Chaos (the clone versions) returns as the Trifecta to ruin their respective counterparts' lives. With Celestia unable to help due to a sickness, can Twilight, Pinkie and RD defeat the Trifecta?
Villains: The Trifecta. Cameo by Dr. Lizardo

Boris Versus the Red Devil: A reformed Boris finds himself facing some major trouble when a real Red Devil comes to Equestria with plans to bring him to Tartarus. His old and new friends fight to keep him despite his past crimes.

A Dragon's Grief: Spike, wanting to prove that he can defend himself, has fled to the Everfree Forest. Can Twilight along with the CMC talk find her assistant/son? And when they run into a town from Apple Bloom's past, can they survive it and Death Rager?
Villains: Deadly Rager, the zombie ponies of Sunny Town

Mama Lizardo: Dr. Lizardo's mother pays a visit and decides to show her son how it's really done. And unfortunately for the good guys, even her son, this mother is more smarter and aggressive than Dr. Lizardo!

A Gravelful of Regret: Is Quartz Gravel really the so-called friend of Royal Slash and Prince Meanie? What happens when Scootaloo is involved in an accident and thus sent to a hospital? Will she, unlike her snob of friendsr, will feel remorse and regret?
Villain: Royal Slash and Prince Meanie

Siblings' Punishment: (shortly after "A Spoonful Of Regret") Royal Slash and Prince Meanie are getting punished severely for what happened during Scootaloo's accident and such. But the duo felt like they were already punished: they lost their best friend to the CMC!

Confronting Gravel and King Nice: (takes place during "a Spoonful of Regret) We all know that thanks to Han Zero, the remaining CMC and Quartz Gravel, Rainbow found out that Royal Slash and Prince Meanie were responsible for Scootaloo's accident, but how did our friends find out in the first place?

Chucky versus Glados: The evil doll Chucky is bad as he has stolen the spell to kill the ponies easier in their dreams. Of course, the lord of Nightmares, Glados, doesn't like intruders like him meddling in his territory.

I'm Not A Slave!: Spike is fed up of being treated like a slave that he locks everypony, including Twilight and Nyx, out of the castle, threatening throw spikeballs at anyone who comes closer. Can the others talk him down?
Villain: Spike (more bitter than evil)

Not A Slave, But A Friend: (After "I'm Not A Slave") After Twilight and her friends manage to convince Spike that he isn't a slave, the baby dragon still doesn't feel so worthy. The gang works on proving otherwise to him.

A Secret Place: Dinky finds a calm, quiet, undiscovered cave which leads her to a beautiful valley. Soon her friends join her to find new secrets in the valley. What sort of secrets will they find? And what will happen when Royal Slash and Prince Meanie wants to destroy this secret place?

Tartarus Unleashed: Smaug and the Apocalypse Ponies open the gates of Tartarus, sending evil all over Equestria and making chaos for our heroes who work 10 times than before to contain it.
Villains: Smaug and the Apocalypse Ponies, the dead from Tartarus

Boys' Trip to Tokyo: (based on an episode of The Simpsons) Ben Mare and the other stallions visited Tokyo on Earth to go on an all-stallions out. Chaos and such pursue!
Note: the Mane Six, Barbara and Luna make a few appearances in this episode.

Pinkie Todd: The ponies put a play about an infamous killer who makes his victims into cupcakes while planning his revenge on those who wrong him. And a certain party pony is in the villain role!
Villians: Pinkie Pie (as Sweetie Todd), Apple Bloom (as Lil' Low), Trixie Lulamoon (as Judge Truilli), Lyra Heartstrings (as Adolf Ponyielli)

What Disney Character Are You?: The ponies decide on a little role playing with Disney characters...and the silliness occurs!
Characters: Belle (Twilight), Beast (Ben Mare), Genie (Pinkie Pie), Goofy (Brian), Mulan (Applejack), Peter Pan (Caramel), Snow White (Fluttershy), The Prince (Dexter), Sally (Rainbow Dash), Lightning McSpeed (Soarin'), Tiara (Rarity), Naveen (Lord Eric), Mushu (Spike the Dragon), the Seven Dwarves (Apple Bloom, Scootaloo, Sweetie, Lorenzo, Pipsqueak, Twist and Dinky Doo), Lilo Pelekai (Nyx), Stitch (Phobos), Hercules (Big Macintosh), Meg (Cheerilee), Angel ( Timon), Swiper (Banzai the Hyena), Han Zero (either Scar or Jafar), Luna (Zira or Maleficent)

The Party Pony and Spider-Mare: Pinkie decides to "jump" dimension and meet up with the Spider-Mare version of herself. But can these two pinkie ponies be enough to stop the newly formed Apocalypse Six led by the once again insane Doc Freeze?
Villains: Doc Freeze (DC Comics), Elecman (Mega Man), Barty Crouch Jr./The Magic Snake (Harry Potter), Grogar/The Goatman, the Chameleon (T.U.F.F. Puppy), and the Helmaroc King (Legend of Zelda)

Trapped in a Safe: (sometime before "Big Brother Team Up) In an accident, Shining, Han Zero and Big Macintosh ends up trapped in a safe with the fillies as well as Cadance, Princess Luna and Cheerilee. As they wait to get out, they did some talking.

Team Big Brother: The Apocalypse Ponies send in their newest member: the evil version of Shining Armor! Teaming up with ??? and Big McMurder, they kidnapped the Mane Six, their boyfriends, Spike and the CMC, prompting Shining and Han Zero to save them.
Villains: Big McMurder, Black Knight (Shining Armor's evil self) and Han Zero

Mrs. Lizardo: Dr. Lizardo still wants Pinkie Pie so he kidnaps the party pony and plans to turned her into a lizard, obedient and under his control. The gang must save her or they will lose Pinkie forever!

Back to a Red Devil: Boris got his horn back, along with his Red Devil powers. But now that he has reformed, will he uses his powers for good or will he get rid of them in return of being an unicorn again?

My Little Pokemon: An accidental spell put Twilight and company into the world of Pokemon where they meet Ash and their friends. Unfortunately, Dr. Lizardo also crosses over and teams up with Team Rocket and Giovanni to capture the rare of Pokemon and the ponies.
Villains: Dr. Lizardo, Wilco, Giovanni, Team Rocket

Trixie's Remorse: Trixie, now living at Castle Canterlot, feel remorse over her actions thanks to being forced to by father Smaug. Will she ever earned forgiveness from those that she has hurt? And what of Warring Malice, her old friend?

Two Dragons, Three Fillies: Spike and Phobos take the CMC out for a overnight camping trip, telling some ghost stories. But things get scarier when it looks like the "Headless Pony" is real!
Villain: The Headless Pony (just the fillies' imagination though)

The Razor Glove Of Freddy: Glados teams up with the evil nightmare known as Freddy Krueger, causing nightmares a-new for the Mane Six and their friends. You thought that was evil? Let's see what happens when we throe Jason Voorhees into the mix!
Villains: Glados, Freddy Krueger and Jason Voorhees

Two Sick Dragons and One Pegasus: Spike and Phobos are caught by some sort of disease which can only be cured by a special flower which is on the other side of Equestria! It's up to Rainbow Dash to get the flower and back or they are goners.

Dashereseque Five: Lucille's Last Stand (obviously the "Dasheresque Five up now, would have to be changed to "Dasheresque SIX: The Next Generation") Lucille is dying, but is determined to try to take Dasheresque and Dasheresque Too down with her. With the help of her bodyguard Stompin' Ya Stallion, her new top underling Montague (played by Lord Eric) and the fearsome assassin Darkfire (played by Han Zero), Lucille launches an all-out final scheme against the heroes. Fortunately, Dasheresque and Dasheresque Too have new allies of their own: the super-heroes Skydude (Soarin') and Captain Random (Brian).
Villains: Lucille (Rarity), Stompin' Ya Stallion (Big Mac), Montague (Lord Eric) and Darkfire (Han Zero)
Pairings: Lucille (Rarity) x Montague (Lord Eric), Dasheresque (Rainbow Dash) x Skydude (Soarin') and Dasheresque Too (Pinkie Pie) x Captain Random (Brian)

The Clone Wars (Star Wars/MLP crossover): Count Dooku and the Separatists decide on striking on Equestria to uses it for their battle in the wars. The Jedi are brought in to help the inhabitants fight them back.
Villains: Count Dooku, General Grievous, the droid forces of the Separatists

Gru! You Pinkie Promised! (a short, almost pure comedy, crossover with "Despicable Me"): While watching "Despicable Me", Pinkie Pie gets infuriated at Gru breaking his pinky promise to Agnes and leaps into the television (well, she IS Pinkie Pie) to make him pay. Using a new type of teleportation spell, Twilight zaps herself and the rest of the Mane Six into the movie to try to calm Pinkie Pie down before anybody gets hurt.

A Deal with Smaug: Trixie comes down with some sort of disease from during her time with the Apocalypse Ponies. Celestia and Mane Six goes to Smaug for help but is there a price to pay for him to save his daughter?
Villain: Smaug

Family Quality Time, Dragon-Style (slight crossover with Generations 1 and 3): Following their adventure in Sunny Town, Spike spend a quiet day visiting with his better, still-among-the-living relatives; namely his grandfather and uncle; both of whom are ALSO named "Spike".
 
A Dinosaur of a Challenge: The Autobots return to Equestria. This time they bring another group of Transformers to Ponyville called the Dinobots. They are group of powerful but dim warriors who can transform into Dinosaurs. Twilight tells Grimlock (The Dinobot's leaders) all about the most powerful creatures in her world. When he goes missing, Autobots and Mane Six decide to look for him. After finding a beat up hydra, they realize what the Dinobot is doing; fighting monsters to prove himself the strongest. Grimlock takes on a green Dragon and Cerberus. While the Optimus and the Mane Six look for Grimlock, the other Autobots have to keep the evil creatures from escaping Tartarus. But Grimlock maybe in over his head when he attacks an Ursa Major.
(Note, Grimlock doesn't kill any of the monsters he fights)

Hush: Ponies are being attacked and injured left and right by a mystery villain known as "Hush". The ponies become the hero known as Mare Do-Well to find out the mystery of this attacker.
Villains: Hush

Mare-Do Well Revealed: In a shocking turn of events right after Hush was defeated, the Mane Six are revealed to be the Mare Do Well, much to Lorenzo's shock. With the ponies becoming big time celebrities, how will they continue their every day activities?

Boxco and Dum-Dum's Revenge: Boxco and Dum-Dum, although reformed, are upset by the fact that two of Boris's old victims tried to kill them. And of course, they want payback. But can these two idiots do anything right?
Villains: Twilight's old school friends who were once Boris's victims of bullying

A Day In The Life Of Dr. Lizardo: Based off a Powerpuff Girls episode. It's another day of the life for Dr. Lizardo, getting his breakfast, reading his newspaper...and planning to destroy the Mane Six once and for all.

Slash Vs. Gravel: Royal Slash wants Quartz Gravel back back but how can she since her former friend has have enough of her bullying ways? The answer: not easy.
Pairings: Apple Bloom x Lorenzo, Nyx x Pipsqueak

One Snob, Two Dragons: After her failed attempt to kill Quartz Gravel the CMC, Royal Slash tries to instead try to get rid of the Dragons, but again, easier said than done!

Smaug's Grand Switch (note: this story takes place a few days or longer before the three-part story depicting Smaug's end): Smaug uses a "body-swapping spell" to switch bodies with Princess Celestia to allow himself access to her superior power as to improve his odds of crushing the Mane Six and their friends (as well as, obviously, taking over Equestria). Celestia, meanwhile, trapped in Smaug's body (which is still powerful, but considerably less so than she's used to in her own body) tries to foil the scheme. But how will the Mane Six and their friends react to "Celestia" trying to destroy them and "Smaug" trying to HELP them.
Villain: Smaug

Whose The Main Duo Around Here?: With the Mare Do Well's identify exposed, Lorenso Magic is more excited to be the sidekick of the heroine more than ever. But which of the Mane Six would he want to be a sidekick to since they are all the same heroine?

Arrogance Removal Spell: Diamond Tiara and Silver Spoon, wanting to put an end to Royal Slash and Prince Meanie's behavior, has Nyx uses a spell to get rid of their arrogance. But will the changed siblings be better than the old?

The Mecha Six: Dr. Lizardo, not learning his lesson, made robotic versions of the Mane Six, with all of their moves and powers. How can our heroes beat something that is metal and knows their every move?
Villains: Dr. Lizardo, Wilco, the Mecha Six

A Gruesome Twosome: A vengeful ??? looks for somebody with the power to help him in his revenge schemes. To that end, he finds Nightmare Moon II and frees her from the stone prison she has been in since her defeat by Spike and the pets of the Mane Six in "All Pets Are Off" (she tried to turn THEM into stone, but the heroes used one of Rarity's mirrors to deflect the stone spell right back at her). The two villains team up to make Spike, Han Zero and their friends pay. However, apart from both being nastier counterparts to former villains and their mutual hatred of the Mane Six and their friends (Spike in particular), they really don't have much in common, so can they keep it together long enough to pose much of a threat to the heroes?
Villains: ???, Nightmare Moon II

Mask Of The Phamtasmare: A mystery figure known as the Phamtasmare is brutally harming bad guys and the Mare Do Well AKA the Mane Six is being held responsible. As they try to find out the identify of this attacker, the ponies discover a connection to the past of their own.
 
Boom!: Parts of Equestria are blowing up due to explosives being laid in certain parts of Equestria. The Mare Do Well goes back into action, teaming up with an old legend while taking down a new foe.

Silver Light: Royal Slash and Prince Meanie has stolen a device from Professor Whack's place and kidnap the former bullies Diamond Tiara and Silver Spoon to steal their light that represents friendship to get them to be bad again.
Villain: Royal Slash and Prince Meanie

Royal Slash and Prince Meanie The Outsiders: Short story. After their previous defeat, Royal Slash and Prince Meanie feels like an outsider due to her actions so far. It's enough to make them regret what they did.

King Nice's Lament: Short story. King Nice, feeling a bit ashamed of his family named being tainted because of Royal Slash and Prince Meanie's actions, wonders how he ends up with such nastyfoals and why he bother putting up with them. Perhaps some love forgotten could explain things to him.

MareFall: For some reason, Iron Will appears to turn evil and begin terrorizing Ponyville, including the Mane Six whose backs he broken! With the Mane Six out of commission for a while, their lookalikes take up the reigns of the Mare Do Wells to stop Iron Will.
Villain: Iron Will (revealed to be a robotic double gone mad)

Another Fine Multiverse Mess (crossover with various Nicktoons and Cartoon Network shows): A freak accident with the dimensional portals of both Dexter AND Jimmy Neutron, pulls them plus several other Cartoon Network and Nicktoon heroes (specifically: the Powerpuff Girls, Juniper Lee, the Alien Force team and Kids Next Door Sector V on the Cartoon Network side and Timmy Turner, SpongeBob SquarePants, Danny Fenton/Phantom and XJ-9/Jenny on the Nicktoon side) to Equestria. While the two boy geniuses (along with Twilight) try to find a way to return everybody to their right universes, an army of villains from the visiting heroes' universes stir up trouble for the rest of the heroes.
Villains: Suffocator Jill, Starven Fran, Mojo Jojo, Him, Princess Morbucks, Auntie Roon, Loki (Juniper Lee version), Vilgax, Father and the DCFDTL, Toilenator (no, seriously), Mr. Boss, Mr. Crocker, Plankton, Plasmius, and Queen Vexus
Pairings: The obvious ones, Timmy x Trixie, SpongeBob x Sandy, Danny x June, Jenny x Brad, Dexter x Blossom

Vernon Versus Freaks: Vernon has caused trouble in Equestria again, but the princesses locked him up in a prison to teach him a lesson. Will the man learns it or will being with the same ponies that he hated make things worst for him?

Royal Slash and Prince Meanie's New Friends: Since Quartz Gravel has turned her back on Royal Slash and Prince Meanie, the brats has gotten some new friends: Mitch, Greedara and Scamward. Can the Cutie Mark Crusaders survive the newly bullying foursome?
Villains: Royal Slash, Prince Meanie. Mitch, Greedara and Scamward

Bad-Time Stories: Some mysterious force is causing the villains from various classic stories to literally come to life and it's up to the Mane Six to solve the case.
Villains: Big McMurder (Big Macintosh's evil self), Miss Terror (Cheerilee's evil self), Granny Witch (Granny Smith's evil self), Apple Blood (Apple Bloom's evil self), Skinnie Belle (Sweetie's evil self), Dr. Jekyll and Mr. Hyde, Frankenstein's Monster, John Long Silver, the Big Bad Wolf, the "Jack and the Beanstalk" Giant, Monstro, Rumplestlitskin, Count Olaf, Voldemort, the Death Eaters
 
The Lost Pony: Fluttershy discovers a little colt named Dusk lost and decides to adopt him like Twilight adopted Nyx. The new pony gets along with the folks of Ponyville, especially the CMC. But five certain bullies wants him gone.
Villains: Royal Slash, Prince Meanie, Mitch, Greedara and Scamward
Pairings: Fluttershy x Dexter

Amacorn Dames On The Prowl: (loosely based on the Futurama episode "Amazon Women In The Mood") Doctor Lizardo traps the Mane Six and their boyfriends in a rocket ship of his own creation and blasts them off toward a far-off world. On this world, our heroes meet an entire tribe of renegade alicorns who were exiled for being much too warlike and being unwilling to take no for an answer concerning handsome stallions. Ben, Brian, Soarin', Caramel, Dexter and Lord Eric all get captured the the Mane Six must rescue their coltfriends and return to Equestria before the stallions end up literally dying from the Amacorns' persistent attention.
Villains: Doctor Lizardo, the Amacorns

One Order of Mad Scientist Lizard Going Down (takes place during the latter half of "Amacorn Dames On The Prowl"): While the Mane Six and their boyfriends fight for their survival and freedom on the Amacorn world, Doctor Lizardo proceeds to try to plunder Equestria to his black heart's content. Not being able to wait for Twilight and the others to return, Spike, the Cutie Mark Crusaders and the pets of the Mane Six try to stop the mad-lizard themselves.
Villain: Doctor Lizardo

My Little Arkham: On the way back from the Amacorn world, the Mane Six and their boyfriend end up in a wormhole and into another universe, right into a part of a city that is now a prison. Now they gotta escape both the prisoners and the TYGER operatives while working with Batman.
Villains: The Joker, The Penguin, Two-Face, various Batman villains

Sweetie's Swan Song: After an incident that was caused by Greedara during one of Sweeties' performances, Sweetie decides to give up singing. Can the CMC and Rarity be able to give Sweetie her confidence back again?
Villains: Greedara 
 
Mare-Do Well Verus Escuro Salvator: One pony, fed up with how crime-riden Equestita is with all the corrupt ones, decides to save Equestria, in his own way by attacking the criminals to the point of death. The Mare Do Well(s) fight to stop this nasty vigilante.
Villain: Escuro Salvator (voiced by Billy Zane; think of his "Ansem" voice)
Note: Escuro Salvator is loosely based on Ra's Al Ghul (from the Batman comics)

Luna's Nightmare: Luna wakes up one day to find nothing out of the ordinary, same sister, same friends...except for the fact that Han Zero has died a week ago! Without her beloved colt-friend, can the Goddess of the Night adapt to this world or will she choose to end it? Or is this all just one sick nightmare?
Villains: Apocalypse Ponies (in dream), Glados
Pairings: Princess Luna x Han Zero

Luna's Lament: (one short set after "Luna's NightMare) After the nightmare made by Glados, Luna is started to feel terrified and doubt for her relationship with Han Zero. Luckily, her colt friend visited and comforts her.
Pairings: Princess Luna x Han Zero.

Duel Of The Fates: Dr. Lizardo, with the help of Fafnir, takes Ponyville hostage. The Mane Six, their boyfriends, the foals and Brave Heart fight to save the village but the story also pits Brave Heart against Fafnir! Who will win in this major battle and will Ponyville be safe?
Villains: Fafnir, Dr. Lizardo and Wilco

Funeral for A Fiend: (based on the Simpsons episode with the same name) After one of his plans of killing the Mane Six failed, Dr. Lizardo appeared to have died and the ponies finds themselves being blamed. But is Dr. Lizardo really dead?
Villains: Dr. Lizardo, Wilco, the Lizard Family

Derpy's Mission: Ponyville is caught in a disease that threatens to destroy every pony there is, even the Mane Six are infected. The only cure is in a town a few miles away and the one pony who can get it...is Derpy!

My Little Pokemon 2: Mewtwo Returns: The events of "My Little Pokemon allows Giovanni to remember Mewtwo, beginning the man-hunt for the clone of Mew again. Teaming up with the revived Tic-Tac, Team Rocket threatens the clone again. The Mane Six and Team Ash teams up to stop them.
Villains: Giovanni and Tic-Toc

Cousin of the Griffin: After a particularly frustrating day of assisting Twilight, Spike heads out the lake. Once there, he meets a friendly Griffon named Bucky. They quickly become fast friends. Bucky knows how Spikes feel because he's boss around by his older Cousin. But things take a surprise twist when Bucky comes for Spike for help. His cousin has been bitten by a Winged Viper (A Winged Viper's bite is poisonous and fatal if not cured). And his cousin is none other than Gilda. Despite that, Twilight and Fluttershy agree to help. With Zecora's help, they make potion can that can save Gilda. They need one more ingredient for the potion to cure her is an ice apple, a rare fruit that grows on the top of The Ice Age Mountains. Only Rainbow Dash is fast enough to get it. But she refuses. Can her friends convince her to help save the life of her former friend?

Captain Fork: Jack Silver has a new enemy trying to steal his treasure: a pirate unicorn with a fork for a hoof named Captain Fork. Can the heroes defeat this friend who is a bit of a mama's colt?
Villain: Captain Fork (voiced by Corey Burton)

This Time, It's Personal: Fafnir has returned and he has harmed Brave Heart's true love Lucky Cover! Brave Heart plans on a quest to hunt his enemy down for payback, taking his friends with him.

Little Macintosh: While his sister and her friends went off to help Brave Heart fight Fafnir, Big Macintosh holds up the fort with some of the others not going, but of course, the Film-Flam uses machinery to make the big stallion smaller in hopes to take over Sweet Apple Acres.
Villain: The Film-Flam brothers

Open Up to Me: Tiara goes out to find Scamward and tries to convince him to leave the bullies. Can Scamward finally reveal his true feelings to her? Meanwhile, Royal Slash and Prince Meanie's nightmares about their "mother" start to overcome them.
Villian: Madam Quartz (mentioned and a brief flashback)
Note: This is the start of Scamward x Diamond Tiara

Training Day: In order to be fully prepared for the fight against Fafnir, Brave Heart shall put himself and his friends through some hard training. Will any of the others make it through in one piece? And do they even wanna continue after the training is done?

The Final Countdown: The time has come to fight Fafnir in a one on one duel to the death. The ponies vs. Fafnir's minions and Brave Heart vs. Fafnir! And trust me, not everyone is coming out of this fight alive!
Villain: Fafnir

Scaward Goes A-Courtin' (happens a little before "Romancing the Enemy"): Royal Slash gets the idea to send Scamward to try to court Diamond Tiara and possibly seduce her into betraying her friends. But it seems like Scamward is developing REAL feelings for Diamond.
Villains: Royal Slash and her gang (Scamward in particular)

The Good Old Days: Be careful what you wish for, Twilight learnt that the hard way when she wished for the days when she never met her friends and was still Celestia's student. But when the filly wakes up, not only did the wish came true, but Nyx never existed and Ben Mare is still missing! Twilight gotta fix this.

A Strange Return: The Mane Six finds themselves imprisoned in an abandoned insane asylum by Dr. Hugo Strange, who somehow ended up in their universe. And the mad therapist is planning on finding out how these ponies 'ticked' by any means necessary.
Villain: Hugo Strange

Romancing the Enemy: It seems Diamond Tiara, despite their mutual claims to the contrary AND despite the fact they are on opposing teams, have major crushes on each other. Can the Crusaders take advantage of this fact to redeem Scamward? Or will Diamond Tiara be seduced back to the dark side?
Villains: Royal Slash and her gang (though Scamward starts showing signs of eventual reform)
Pairing: Diamond Tiara x Scamward

Lorenzo the Mighty: Wannabe super-hero Lorenzo ends up gaining actual super-powers via a freak magical accident. Of course, he decides to use these new powers to better help others and to impress Apple Bloom. However, the Mane Six have a super-hard time keeping up with the super-colt and trying to prevent him from getting hurt when the spell that gave him his powers eventually wears off.
 
Songs Galore (kinda based on a Simpsons clip show): After watching a musical, Rainbow thinks that songs in movies/shows are completely pointless. Her friends decides to prove her friend by explaining the songs that the ponies has sang over the years.
Songs: Songs from Seasons 1, 2, 3, 4, and 5.

The Ultimate Enemy: After getting captured and tortured by the Apocalypse Ponies, Twilight finally snaps and she turns into a dark version of herself, threatening all of Equestria. Can the Mane Six, her friends, Ben Mare, Celestia and such change her back or is it too late for her?
Villains: The Apocalypse Ponies, Dark Twilight Sparkle

Trip To Gotham: Part 1 of 2. The Mane Six and their friends return to the world of Batman and the Mare Do Well makes her appearance, teaming up with Batman on a mysterious case!

Back to Arkham City: Part 2 of 2. One of Batman's enemies kidnapped Twilight Sparkle with plans on using her power to take over Gotham. The good guys must go into Arkham City again to save her before it's too late.

Mitch vs Lorenzo: Mitch challenges Lorenzo to a fight to prove that "blank-flanks" are weak against others with cutie marks. Will Lorenzo be able to prove him wrong?
Villians: Mitch, Scamward and Greedara

Scarecrow's Attack: The Scarecrow, learning about Equestria from Dr. Hugo Strange, manages to crossover to there and release his fear gas on the ponies. Now the ponies must conquer their worst fears to stop Scarecrow.
Villains: Scarecrow (DC comics), the ponies' fears

Spike Gets Schooled: Twilight decides that Spike will be attending the Ponyville School so that he can learn and be educated better. Will the baby dragon survive the whole thing?
 
Cadance's Wrath: Cadance is about to give birth again to a new foal. But when the princess has mood swings during the pregnancy, trust me: things are going to get nasty in a hurry!

The Incredible Stare: A new stallion came into town and appears to want to challenge Fluttershy to a staredown, having the power of the Stare! And when she fails, it's up to Nyx to step in before this new stallion uses his power to terrorize Equestria.
Villain: The Stare-Master

The Hangover: The Mane Six gets one nasty hangover after drinking a lot of Apple Cider. Now they got to recall what they themselves did to avoid a huge disaster.

The Hangover: Dragon Style: (takes place during "The Hangover") The ponies aren't the only one who got a nasty hangover. So are Spike and Han Zero! Now they got to recall what happened as well to save their relationships with Barbara and Princess Luna!

My Little Freelance Police (crossover with Sam & Max: Freelance Police): Somepony has stolen the Elements of Harmony. Pinkie Pie tries to find a detective to solve this case. But all she got was a 6-foot anthropomorphic canine detective dressed in noir-styled suit and hat and easily excitable 3-foot "hyperkinetic rabbity thing". They call themselves Sam & Max: Freelance Police! Can they solve this case? Or are they more trouble than they are worth? And who stole the Elements of Harmony? And why does Pinkie Pie go on about something called My Little Freelance Adventurers?
Villains: Mack Salmon, Dr. Lizardo, Wilco, Crarity, Liarjack, and The Mare-Do-Rotten

The Final Death: The former zombies ponies of Sunny Town try to find ways to redeem themselves for their crimes of murdering Ruby long ago. Will they even get forgiveness from Apple Bloom? And will Grey Hoof get forgiveness from Ruby and Zecora?

Dogs, Cats, Rodents, Bugs and Ponies! Oh My! (crossover with "Krypto the Superdog" and "Chip N' Dale Rescue Rangers"): When powerful extra-terrestrial villains invade their turf and enhance the abilities and technology of animals criminals across the world, the Rescue Rangers call in Krypto, Streaky and Ace for back-up. The resulting fight causes all the animal heroes (as well as Fat Cat and Isis) to be transported to Equestria and transformed into ponies (except for Zipper, who is turned into a dragon). In the past, Krypto, Streaky and Ace have assisted the Mane Six as have the Rescue Rangers. Can our heroines return the favor and help the animal heroes get back to and save their own world?
Villains: Emperor Techmeeon (an OC villain; a very powerful and very intelligent space villain who happens to rule his own galaxy and loves to use his abilities and technology to make those who faithfully serve him MUCH more formidable), Fat Cat, Isis, Smaug, the Apocalpyse Ponies.
Pairings: All the usual ones place Fat Cat x Isis
  
Time's Hour At Hand: An entity named Time, felt not appreciated, begins to mess with time and endangering the ponies' lives. The Mane Couples, their allies and the princesses must speak sense into him somehow.
 
A Trip Into Cyberspace: The ponies get sucked into cyberspace where everything can happen, along with security sites who has mistaken them for viruses and want to delete them! Can they escape the cyberspace?

Dark Macintosh: Rainbow Chaos uses her discord powers on Big Macintosh, turning him discorded and mad, to attack the other ponies. How will the ponies, especially Big Macintosh's love Cheerilee, be able to restore him?
Villain: Rainbow Chaos

Of Pirates and Princesses: Jack Silver returns to Equestria and it appears that he and Celestia are patching things up. The princess wants to be back with him but still has feelings for Optimus Prime. Will Ben's (spoiler) parents get back together?
Pairing: Jack Silver x Princess Celestia

Celestia's Choice: (short story; takes place during "Of Pirates and Princesses") As Celestia is having fun while being reunited with her old flame Jack Silver, the princess ponders a choice. Will she wait for Optimus Prime to return or go back to a love she lost?

Island of the Giant Ponies: The ponies and dragons' boat trip ends up in a wreckage on a mysterious island where they meet up with giant ponies. Can they escape the trouble and/or make peace with the giant ponies?

A Changeling's Love: Rarity (from Ponyville B) came to Ponyville to introduce her new fiancee to the Mane Six. However, they found out that he's actually a Changeling send by Chrysalis to take Unicornia. But is this Changeling's love fake or for real?
Villains: Chrysalis and the Changelings

Rarity's Selfishness: Photo Finish is finally recognizing Rarity's talents as a model and decides to hire her. The white unicorn lets fame gets to her and charges her prices up for her services, alienating her from her friends, especially Lord Eric.

Jabberwocky Mayhem: For centuries, the Jabberwocky was thought to be a legend. That is until one appears in Equestria, causing even more terrible. Who could stop it? And why are the Apocalyse Ponies helping it?
Villains: The Jabberwocky, The Apocalypse Ponies

For Whom The Bells Toll: It's time for Jack Silver and Celestia to finally getting married, but will their son Ben Mare recover and enjoy the fact that his parents will be together? And why is he so nervous for his relationship with Twilight?

Dark Aura Means Bad News: Part 1 of a 2 part story. There are some new ponies in Equestria who appears to be nice and friendly. But the Mane Six, the Stallion Six, the CMCs and the dragons don't trust them for some reason.

Hellfire: Part 2 of a 2 parter: The 'nice' ponies are demons from Tartarus who send the heroes to Tartartus itself to keep them out of the way. Now the good guys got to escape before the demons absorb the good souls of Ponyville.

Betraying Your Father: Smaug, having enough delays, goes after Trixie himself, wanting to either force her back into the Apocalypse Ponies or kill her himself. The unicorn must put aside her fear of her father and stop him.
Villain: Smaug
 
Two Dragons, Two Universes, One Adventure (crossover with the Spyro series): Spike, by means of a mysterious vortex, somehow end up in another universe and end up sharing an adventure with a dragon hero by the name of Spyro in an effort to get back home..
Villains: Ripto, Gnasty Gnorc, the Sorcerer, the Sorceress, Grendor
 
Science Vs. Friendship: Dr. Lizardo is going on an all-out war on the Mane Six, using whatever machinery he got to crush them once and for all. And now, the Mane Six must face him in a duel which poses the question: Science or Friendship.
Villain: Dr. Lizardo

Beam Swords or Lightsabers: The dragons and ponies have this question in mind: which is better: beam swords or lightsabers. So it's time for them to try the weapons out.

Fluttershy and Rainbow Dash in Cinderella in Wonderland: Flutterhsy tries to get Rainbow Dash to read her new favorite book, Cinderella in Wonderland (Written by Orange Ratchet). Rainbow Dash refuses to read because it's boring and too silly. Sweetie Belle (not learn her lesson from the mess with Ahuizotl), tries another advance spell. This time she ends up sending Fluttershy and Rainbow Dash into Fluttershy's book. Now they go along with Cinderella and Sora as they try to find a way home.
Villain: Queen Maleficent
Pairing: Sora x Cinderella
 
Captain Blackhoof's Revenge: (takes place before My Little Transformer 3: The Dark Alliance) Jack Silver is happily living with Princess Celestia in Canterlot. Part of him still miss life on the open sea and yearns for adventure. Then Jack gets a letter from Twilight informing him that Ben Mare has been Ponynapped. They only clues are a flying pirate ship that was seen on the night of Ben's disappearance. And a pirate dagger left at the crime scene. Jack knows whose behind it, his worst enemy; the legendary and ruthless Captain Blackhoof, a Unicorn pirate who is as cruel and evil as Jack is kind and noble. He is a great sword fighter (according to Jack, he can't so say no to a one-on-one sword fight), a brilliant mechanical genius, and a master of Dark forbidden voodoo magic. Now Blackhoof wants to fight Jack one last time.
Villain: Captain Blackhoof (He's based on Backbeard from Pirates of the Caribbean: On Stranger Tides)
Pairing: Jack Silver x Celestia

Harmony Across the Multiverse (crossover with the "My Little Heroines" series): The Mane Six receive still more other-dimensional visitors. This time, most of them are alternate universe versions of previous visitors, but, at the same time, oddly similar to the Mane Six themselves. Unfortunately, a certain "Ghost with the Most" thinks it would be a funny idea to unleash Discord the evil version yet again and team up for double the chaos.
Villains: Discord II, Beetlejuice

Discord's New Prison: (takes place after "Harmony Across the Multiverse") After the evil version Discord's failed alliance with Beetlejuice, Celestia and Luna decided that instead of turning him into stone again, they send him to a prison that's impossible to escape: the Impossible Zone. But of course, even Discord thinks that won't hold him.

Swipe-Gaia: Swiper, trying to get Angel this time, stole a machine from Professor Whack and made himself powerful, fast and strong. Unfortunately, it also drove the fox mad, putting Equestria in danger.
Villain: Swiper/ Swipe-Gaia (voiced by Marc Wiener and Roger L Jackson

Bumblebee The BBBFF: It's Nyx's birthday again and the Autobot Bumble Bee makes a surprise visit. Things are fine until Nyx calls Bumble Bee her B.B.B.F.F (Big Brother Best Friend Forever). Spike get a little jealous.

Nyx's Uncles: (after Bumblebee the BBBFF) After Nyx's birthday, the dragon want to make up for his jealousity towards Bumblebee by taking him to a special place. What could it be?

My Little Pokemon 3: Giovanni is back along with Team Rocket, using some sort of Psychic-Type Pokemon to brainwash little foals, even the CMC and Nyx, to turn against the grown up ponies. Ash and his friends return to help the Mane Six solve this mystery.
Villains: Giovanni, Jessie, James and Meowth (Black and White personalities)

The Eighteen Mane Sixes: The Mane Six meets two versions of themselves from two versions. The eighteen heroines team up to stop their enemies who has been gathered by a new foe.
Villains: Chrysalis, Night Dragon and The Anti-Magic, The Dusk (secret identity and role as main villain revealed at the end the end; debut and only appearance voiced by Tara Strong)

Megan's Return: Megan decides to take a vacation with her family to Equestria to have some fun along with peace and quiet. The ponies, despite some problems, intend on giving their human friend the best vacation ever!

Dora The Explorer: Lost In Equestria: Swiper's past came back to haunt him as his old friends Dora and her pals arrive in Equestria. And with his new behavior, the ponies must keep their new friends safe at all cost.
Villain: Swipe-Gaia

Spike and Bucky's Awesome Trip: Celestia gives Spike the task of delivering the Phoenix's Heart, a priceless ruby to the Manehattan museum. But Twilight and her friends are too busy to join him. But luckily Bucky the Griffon is free to join him. Also the Diamond Dogs wants the Phoenix's Heart too. Can these two outwit the Diamond Dogs and get the Phoenix's Heart to the Museum?
Villains: The Diamond Dogs

Who Shot Dr. Lizardo: (loosely based on "Who Shot Mr Burns") Dr. Lizardo has begins strengthening a hold onto Ponyville from stealing the Apple Cider, damaging buildings and blocking off Celestia's sun. But when someone shot the villain, the ponies must find out who is the shooter.

Discord Vs. Chaos: Discord the evil version, furious over his daughter Eris's betrayal, makes an ultimatum: cause never ending chaos to all of Equestria or watch her friends suffer. Will Eris be forced to give in?
Villain: Discord (evil version)

A Hunter's Redemption: A month after he and Trixie ran away and changed sides, Boris feels like his evil ways in the past ruined his good name as a hunter. Trixie tries to convince him to consider otherwise, but Boris still feels guilt for what he did long ago. It's up to Twilight, Ben and Trixie to get him back on his feet, before he does something to affect himself, Trixie and all around them in a life-damaging matter.

The Last Cyber-Pony: During a clean of a forest, the ponies found what appears to be a Cyber-Pony who seems harmless. After what happened before, will the ponies decided to give this one another chance?

Tiny Trio Trouble: Apple Blood, Skinnie Belle and Brutealoo (Scootaloo's evil self) join forces to torment their good counterparts (and, by extension, their counterparts' older siblings and idol) by framing the Cutie Mark Crusaders for despicable acts. Will the trio be able to clear their names and defeat their evil counterparts?
Villains: Apple Blood, Skinnie Belle and Brutealoo

Forbidden Love: It was bound to happen sooner or later. Lyra and Bon Bon became a couple, but that type of love is frown upon in Equestria. Can their love ever work or will it be for naught?
Pairing: Lyra x Bon-Bon

The Mare In Black: A mystery mare comes to Ponyville and suddenly the ponies end up getting a bit ill. The CMC and company suspects that this new Mare in Black is responsible for but will they prove it? And if it isn't her, then who is responsible?
Villain: Count Horseula

As Mad As Pinkie: It's a Mad Pinkie World as everypony is beginning to act like Pinkie, even Pinkie's friends and the princesses are acting crazy. Pinkie Pie and Brian, the only ones not affected, work on figuring out how to solve this crisis.

The NightMare Sun?: The stress and pressure, along with the fact that Luna is becoming more popular than her, is too much for Celestia to handle as she ends up going crazy, turning into Solar Flare. The Mane Six, their friends and Jack must find a way to snap her out of it before she consumes all of Equestria!
Villain: Celestia/Solar Flare (she's temporarily insane)
Parings: Jack Silver x Celestia

Such a Weak Princess: After what has happened, as well as the Solar Flare incident, Celestia felt too weak and useless to continue on as ruler of Equestria. Her true love Jack Silver helps her along with some other help.
Parings: Celestia x Jack Silver and various

Memories of the Chaos: After getting Celestia back to normal a small tiny filly is discovered. Will she end up being like Nyx was before or will she be saved?

Nyx and Selena: After Selena (the filly version of Celestia's darker self) is successfully rehabilitated by the Couples Six, Spike and Barbara, she starts to get used to her older sister, Nyx, and vice versa.

The Death Lizard: Dr. Lizardo release his deadliest creation: the Death Lizard which could wipe out half of Equestria's population in half! Now the Mane Six must invade the space station to put it out of commission!
Villains: Dr Lizardo, Wilco and the Death Lizard Robot (based on the Death Egg Robot)

A Fallen Rainbow: An accident ends up hurting Rainbow's confidence to the point that she decides to never fly again. Will the Pegasus pony stay grounded or will her friends help her get her confidence back?

Faces In The Mirror: Something is wrong with the ponies of Equestria, they are acting strangely and even more violent, especially Twilight and her friends. As it turns out, to Nyx and the foals' alarm, that the real ponies are taken to the mirror universe, replaced by demonic mirror versions of them!
Villains: The mirror versions of the ponies

Avengers Assemble!: Smaug has taken away the Avengers' powers, turned them into ponies and whisked them away to Equestria. There, they meet their old friend Rainbow Dash and the rest of the ponies. Now they must work together to get Smaug and retrieve their powers.
Villains: Smaug and Fluttercruel (resurrected by Smaug)

No More Parties: After 1 of Pinkie Pie's parties went too far to the point of chaos, Mr. and Mrs. Cake told Pinkie not to do anymore of them, or in this case to the point of that happening again. This saddened Pinkie Pie, who misunderstood, to the point that she can't work or do anything anymore.

The League of Chaos: Discord (evil version) and Beetlejuice are joining forces again, this time, they got a new friend: the Joker! With this new wave of chaos, can our pony heroes survive?
Villains: Discord (evil version), The Joker, Beetlejuice

Blooming Lorenzo: After various mis-steps, a considerable degree of unfortunate delays and a streak of just-plain bad luck, Lorenzo finally goes on his first date with Apple Bloom. Just how will it go?

MLP Heroes: (based on Sonic Heroes) Teams goes out on various missions, fighting their enemies and sometimes each other to confront some old foes and save the day in time
Teams: Team Sparkle (Twilight Sparkle, Nyx and Pinkie Pie), Team Ben (Ben Mare, Brian and Dexter), Team Fashion (Rarity, Lord Eric and Fluttershy), Team Apple (Applejack, Big Macintosh and Caramel), Team Rainbow (Soarin', Rainbow Dash and Spitfire), Team CMC (Scootaloo, Apple Bloom and Sweetie Belle), Team Dragon (Spike, Phobos and Barbara)
Villains: Dr Lizardo (Team Sparkle) , Wilco (Team Fashion), the Flim-Flam Brothers (Team Apple), Swiper (Team Fashion), ?, ?, ? and the Mecha-Six (the true masterminds)

A Troublesome Irken: Zim's new machine has teleported him and GIR to Ponyville. Now he plans to take over but how can he do that when GIR only wants to make friends?
Villains: Zim (although he's more of a comedy villain than an actual threat)

Metal Gear Ponies: Information TBD.
Villains: Liquid Snake and Dr. Lizardo
  
That's it for now. Until I can think up more story ideas, have a nice day!