Ultimate Alliance: Villains of Equestria

by PhoenixFlambe


The Calm Before the Storm

On a fine and warm morning, stood the Princess of Friendship on the balcony of the Canterlot Castle. One year has passed since Twilight's ascension to the Canterlot throne, and now she overlooks the entirety of Equestria. Of course, as a Guardian of Harmony, she wasn't alone. Her friends Applejack, Fluttershy, Pinkie Pie, Rarity and Rainbow Dash will stand by her side wherever and whenever the need arises.

Together with Spike and them, they formed the Council of Friendship, which has now expanded thanks to Spike and her many friends reaching out to the other nations. Aside from the ponies of three kinds now also includes the hot-headed dragons, the headstrong yaks, the compassionate changelings, the fiery kirins, the gallant griffins, the noble hippogriffs who are also the fun-loving seaponies, the determined buffaloes, the stalwart deers, the playful Abyssinians, a race of anthropomorphic cat people, the dazzling diamond dogs, a friendly herd of the abadas, watery kelpie and zebras, the temperamental and tiny Breezies and the high-soaring Ornithians, Celaeno's race of anthropomorphic birdmen.

About three months ago, Twilight has sent her friends on four different expeditions to other parts of the world. The mission was to connect with the other kingdoms to establish a strong bond and diplomatic relations between them.

Applejack, Zecora, Rockhoof and Tempest Shadow were sent to Zebrat, Zecora's original homeland in the faraway country of Farasi. Upon docking at the port of Zebrat, the group were greeted by Zecora's original group of friends. They consist of two abadas, two water kelpies and a zebra. Dust Devil was the brown abada with blazing super speed, Cactus Rose was the lime green abada who can speak to plants, Medley Brook was the cheerful wavy-haired kelpie, Crystal the sassy, punk-haired kelpie and finally, Marini, the zebra with the pink streaks in her mane. The latter also being the mayor of her hometown. While unsettled and distant at first, Zecora has since warmed up to her old friends and has since being trying reconnect with them.

Next up, the second group consists of Capper, Discord, Pinkie Pie and Trixie. These guys were sent to Capper's old home, the capital of Panthera. Since the invasion of the Storm King, the current ruler of the place, Meowmeow Cat has since outlawed magic and turned the entire city into a police state regime, coupled with anti-magic technology of their own that prevented even the great and powerful Lord of Chaos, Discord from using his powers. Initially arrested on sight and failing to convince the king otherwise, the group were rescued by Capper's old pals. Shadow was the black cat leader, Max the silent muscle, Admiral Fluffington the most dapper of all, Molly the kid and to Mr Dapperpaws' own surprise, his old buddy Chummer, who gained an eyepatch while trying to oppress the regime. After discovering the tyrannical king's ulterior motives, Capper and friends had brought a stop to his plans and since then the king was arrested and nowhere to be seen again. Currently, a new government was to be reformed and revised by Shadow to be able to rule with fairness once more.

The third group of Rarity, Big Mac, Maud Pie and Meadowbrook were sent to Caninia, Dimondia's hidden sister kingdom to resolve a friendship problem between the two opposing rulers of the split and divided kingdom. One of them were occupied by the stern Katherina Proudpaws, the reserved Indiana Embereyes, and one of the twin golden labradors, Fiona Floppyears. The other was ruled by a compassionate Jennino Lanternlight, the optimistic Moonbeam Twinkletail and the other golden labrador twin, Ambrosia Muffinbuns. Both sides have conflicting interests, but thanks to the efforts of Rarity and her group, they were able to get the royal sisters to reconcile. Furthermore, they've since stayed in Jennino's castle due to the old one collapsing out of age and disrepair. Currently, both the Abyssinians and Diamond Dogs are setting up a peace treaty while Spike attempts mediation and reconciliation between the two rival races. It was a rocky road for the little drake though Twilight has faith that he can do it. Spike promised that he will never let her down and will be by her side till the very end. Until then, it was a work in progress.

Finally, the last expedition takes the final group to Ornithia, home of the bird people and Captain Celaeno's original homeland prior to the Storm King's invasion. The group involves Celaeno, her pirate crew, the secret agents Bon Bon and Lyra, the brash but loyal Rainbow Dash and her Wonderbolt captain Spitfire. What initially was a simple task turned complex when Celaeno met the king and queen of Ornithia and their family. They were King Thaumas and Queen Ozomene, their son, Prince Aello with his wife Princess Zephyra and Princess Ocypete. Her, Aello and Ocypete were friends since childhood, the latter apparently about to get engaged with Prince Huginn, a raven. Initially suspicious of the black-feathered prince, Bon Bon and Lyra snuck and followed after him to his private chambers where it turns out, he was never a real prince, and the upcoming engagement was part of a bigger setup by some unknown party. After the agents reported to Celaeno, which the parrot captain then fought and nearly died from the treacherous faux prince, he was discovered by the royals and Rainbow's gang and has been imprisoned ever since within the dungeons of Ornithia. After the whole ordeal, Celaeno and Ocypete made up and became lovers after Celaeno revealed her feelings for the African Eagle princess. Thaumas also apologized for causing trouble for the parrot back in the day and since then, quite recently, Celaeno, her crew, the king, queen, their daughter-in-law and her childhood friends have begun their own personal voyage, leaving the kingdom in charge by their own captain of the guard.

Throughout all the expeditions, Twilight and her friends all discover one thing. A Tree of Harmony, or rather, four more of them. Furthermore, they aren't really the Trees of Harmony as they actually have different names as stated by Ocypete when she and Rainbow's group went deep into the castle chambers and discovered ancient markings engraved on the chamber walls. The lands of Farasi has the Tree of History, the former twin kingdoms of Caninia the Tree of Family, the Tree of Purpose in Abyssinia and finally, the Tree of Love in Ornithia's kingdom. Funny enough, the latter tree was the thrones where the Ornithian family sat on, with Celaeno being a part of the third pair of lovebirds, represented as Hope and Perseverance. Just like the Elements of Harmony, the rest of the other trees too had bearers. Those were, Zecora and her old friends, Capper and his pals, the six royal diamond dog sisters and Celaeno and the Ornithian royal family.

Twilight wonders if she, her friends, the Pillars, her students and the four chosen groups can be Guardians of the Elements, could the rest the world too?

Throughout her journey as Celestia's protégé, she has came to learn the most valuable lesson of them all. Friendship truly is magic. And she's going to share that with the rest of the world.

As her mind ponders, a high-pitched voice called out to her from behind. It was Spike, Twilight's dragon companion and appointed personal advisor and mediator of many neighbouring nations.

"Twily!" Spike called.

Currently, he's attempting to mediate peace between the Abyssinian Cats and the Diamond Dogs. It was a rocky road, but Twilight has faith he can do it.

Hearing his voice, the Princess of Friendship turned around to face him. Accompanying him are Twilight's friends, Applejack, Fluttershy, Pinkie Pie, Rainbow Dash and Rarity. Star Swirl the Bearded and her personal bodyguards Tempest Shadow a.k.a Fizzlepop Berrytwist and Flash Sentry were also present with them.

"Spike! Girls! Star Swirl! And my self-appointed bodyguards! You're all here! And only my BBBFF can call me that Spike, you know that."

"I know, I just wanted to surprise you. And besides, aren't I part of your family too?" said Spike.

Twilight giggled.

"Of course you are! But not just mine, but theirs too! It's like we're one big happy family!" she exclaimed.

Applejack shuddered, remembering when she had to take care of her huge "family".

"As much as I don't wanna take offense to that, that thought of what happened when you tried to share your Friendship Journal still shakes me," seethed Applejack.

"None taken," grinned Twilight as she sweeps her hoof in the air, "besides, what more can a friend ask for?"

Pinkie then extended her front legs around the entire group as she pulls them in for a big, tight, embrace.

"How about a really big hug?!" exclaimed Pinkie Pie.

Tempest and the rest struggled against the squeezing group hug.

"Can't....breathe...." gasped the black-suited unicorn.

"Oops! My bad!" apologised Pinkie as she lets go.

The group gasped and wheezed as they catch their breath. Spike then had something to say to Twilight.

"Today's the big day," he said, "it's also your big day."

"It sure is," Twilight nodded, "the day when the power of friendship triumphs over the forces of darkness!"

Everypony and Spike cheered.

"Although.... Do you think....? That it could have went differently?" continued the princess.

"Whatever do you mean?" questioned Applejack.

"I mean, is there any other way than petrifying these three felons?" asked Twilight.

"Twilight," answered Applejack with a serious expression, "they're bad guys, it's what they do. Not all of them can change or want to."

"I know, it's just.... What they did was unacceptable, but have we ever asked why they did it? Do we even know where they came from?" asked the princess again.

"Twily," Spike replied, "Sombra tried to mind control the entire population into his expendable army, Chrysalis tried to tear my wings apart, Tirek wanted to drain magic and destroy Equestria with it and Cozy Glow wanted to weaponize friendship and rule under her iron hoof! It doesn't get more simple than that!"

"I don't know...." doubted Rarity, "I can't put my hoof on it but back when we fought Sombra when he returned, I feel this small glimmer of light from him. Like, some sort of sparkle."

"A small sparkle in the heart of a pony who's heart is as black as night? Now there's something you don't hear every day," quipped Flash, "I bet he isn't even a normal pony at that point."

"You know, Twilight does have a point," agreed Fluttershy, "I mean, in spite of everything Discord did, no matter how bad or how many times he's done it, I still have faith in him."

"Your faith must have been misplaced," said Tempest with a smug look on her face.

The other ponies and Spike glared at her, unamused at the quip she made.

"Okay fine, bad joke. But I am inclined to agree as well. Had it not for your compassion, Princess, I would be resting in pieces. Literally."

"I can't just stand there and watch you perish, Fizzlepop Berrytwist. I had to do something, " affirmed Twilight.

"And for that, I'm forever in your debt," thanked the orchid unicorn.

"I can also see the good in you, you are not the ruthless lieutenant you think you are, you are just...lost," Twilight reassured.

"But still, I ask and specifically requested to be punished accordingly. Starlight did too. But instead, you....threw a party?"

"A don't-worry-we-won't-hold-it-against-you-no-biggie-no-takebacks-and-we-forgive-you party!" yelled Pinkie excitedly.

"To this day, I still feel regretful of what I've done. So does Starlight and so does Sunset. I don't think I really deserve this. This position as your personal bodyguard. What if I betray you?"

"That's an if, but what matters is you're one of us now."

"I know....but still, sentencing a filly to stone? What if it had been Apple Bloom? Applejack's little sister?"

"Now hold up, leave my sister out of this!" retorted Applejack.

"Anything can happen! How are we so certain it won't? Can't we like use a foresight spell or something?"

"Much like time travel, I'm afraid spells like these or similar are forbidden," answered Star Swirl, "In that case, we can only hope for what's coming."

"Twilight, I'm just wondering, have you done a background check on Cozy? Did you call her parents? What do they think?" Fluttershy asked.

Twilight only looked down and sighed, before saying, "I would love to, but I don't even have a trace as to who they might be, I can't find information anywhere about them."

She sighed again before continuing, "We'll worry about that later. For now, we have an event to tend to."

"If you say so," accepted Fluttershy.

Before anypony could react, Twilight ran and jumped off the balcony.

"Catch you later!" she exclaimed excitedly.

"Twilight!" exclaimed the group in horror as they ran towards the edge of the balcony.

Rising from beyond the fence was the Princess of Friendship herself, flapping her wings and only smiling dorkily at them.

"Relax girls, and guys, did you forget that I have wings now?" reaffirmed Twilight as she did a twirl to show them off.

"What, pffft, of course I know that, I wasn't scared or anything, I'm just worried," said Rainbow Dash.

"Thanks Rainbow, race you there?"

"You betcha! I'm always up for a challenge!"

With that said, the blue fast pegasus and the nerdy alicorn then raced to the ground level of the castle grounds. Meanwhile, the rest of the group simply head back and took the stairs downwards, happily chatting away.


In front of the statue of the Terrible Trio laid a podium with a microphone for the princess to speak into. Gathered in front of the podium was a huge crowd of many ponies and other creatures of different kinds. They were busy chatting away until Twilight, her friends, Star Swirl and her bodyguards Tempest and Flash arrived. Both Rainbow and Twilight made a fancy landing, aweing the crowd before them. The purple alicorn then trotted up the stairs of the podium to make her speech, more confident than the previous ones she gave before.

"Fillies and gentlecolts! Bovines and reptiles! Cats and dogs, avians and other magical creatures out there! Welcome! To the Second Anniversary of Evil's Demise! Here, we celebrate the day we and the entirety of Equestria defeat the three dastardly villains that threatened us time and again!"

The crowd cheered.

"For those new to this celebration, let me break down to you the three of the worst criminals one by one, starting with Chrysalis."

The audience cheered again.

"Queen Chrysalis, a dark changeling whose selfishness knows no bounds. She tried to steal love, replaced all that you know and love and worst of all, she used her own kind like chess pieces to further her goals. They're expendable to her. No mother should've done that!"

The crowd then booed, including the reformed changelings and excluding some of the mothers that attended this event.

"Ouch, way to rub it in like that," whispered Rainbow Dash into Applejack's ear.

"My mom ain't like that, I think," the country mare replied hesitantly.

"No offense to the moms out there. Including you mom! I love you!" assured Twilight brightly.

"Next, there's the greedy centaur Tirek. He tried to take all of Equestria's magic! And ate it!"

The crowd gasped.

"And once he did, he was going to use it and destroy everything in Equestria!"

They gasped again.

"He even manipulated the Lord of Chaos into siding with him!"

Three of the mares in the crowd then fainted from the shock overload.

"Thankfully, it was due to the efforts of me, my friends and even Discord that we've made up and gotten back on our side that we prevented this. This is his final retribution," said Twilight as she pointed at the statue behind her.

The crowd cheered once more.

"And finally, the most vile of all. Cozy Glow. She manipulated with disturbing efficiency the entirety of the three pony races to go with her and yet against each other and took away the land's magic as well. Friendship is not power. It's a skill we need to have in life and is not to be abused. We taught her that the hard way and for that she's imprisoned with her co-conspirators in stone. And with that, the land of Equestria is safe once again! Hip hip hurray!"

The crowd was silent this time, with only the sound of crickets chirping instead. The purple princess was slightly surprised at the lack of reaction.

"Ooooookaaaaaay.... But we saved Equestria and ensured peace! Right?" she announced, hoping to get some creature cheering at her.

Instead, a unicorn mother only snapped at her.

"Is my foal gonna be alright?! Will he be sent to Tartarus if he gets bad grades??"

"Or painting on the walls??" a pegasus father shouted.

"Or drooled in your coffee??" an earth pony mother yelled as she lifts her drooling baby filly in her hooves in the air.

Twilight reeled back at the comments they made before asserting, "What?? No! They're just foals!"

"Then why's she in here?? Had it not occur to you that you could just send her for corrective training and contact her parents?" a stallion asked anxiously.

"I.... Didn't have a choice! And besides, I don't even know who her parents are!" retorted Twilight.

"Not even Celestia nor Luna would do that no matter how stern or cold they look!" shouted another stallion.

"Are you sure about that? Cause I heard it really was the princesses and that dastardly draconequus who imprisoned them!" claimed another.

Every creature including Twilight and her friends all gasped in shock.

"Who told you that?!" demanded the Princess of Friendship.

"Weeeeeell, a little filly told me. She's a pegasus with curls like that statue over there. Only without the freckles and that her mane is blonde and not light blue."

"Hold on," said Fluttershy, "I think I've seen her in the School of Friendship before. I think her name is Cr-"

But before Fluttershy could finish, she was cut off by a blast of raw magic aimed at the statue, destroying and crumbling it into dust and pieces.

Everyone looked at the rubble in utter shock. Twilight gasp in sheer terror, thinking that with the statue demolished, the Legion might be dead.

"Nononononono, no, no no!" trembled Twilight, "The statue! The trio! It's....gone.... Who would do such a thing?!"

"I would," growled a deep voice from behind the crowd.

Twilight Sparkle and her friends looked beyond the audience as they themselves turned behind to see who that voice was. And when they all did, they couldn't believe their eyes.

Standing menacingly behind the crowd was a sight they fear all too well. There stood Lord Tirek, Queen Chrysalis and..... Grogar? The crowd dispersed, screaming in terror and running for their lives once they saw them.

"It can't be...." shuddered Star Swirl.

"Is that...." continued Tempest.

"Discord?! Are you serious right now?!" fumed Fluttershy.

Grogar, Tirek, Chrysalis, Twilight and her friends all look at her with a confused look on their faces.

"How many times must I teach you to always think before you do something drastic?!" continued the peeved yellow pegasus, "You've already freed three of the worst villains out there just to boost Twilight's confidence when it was already going smooth!"

*sigh* "Look, I know you're better than this, Discord. I know it's in your blood and nature to cause mischief among the community. But for once, I think you need to tone down on the ways you've been causing it, because it is doing more harm than good. I know you can do so much better than this. You just have to....try, you know?" pleaded the cream pegasus.

Instead however, Grogar simply zapped at her with a magic bolt, sending her tumbling into the ground.

Twilight and her friends gasped in shock at the sight of Fluttershy getting hurt, before turning to the villains with disgust on their face.

"Discord! Have you gone bananas?!" yelled Rainbow Dash, "I get that you want the trial to be immersive but, that's just too much! Even for you!"

Suddenly, the real Discord popped out into the scene, visibly irritated at the commotion.

"Crimeny! What's with that racket out there?! And who's been calling my name?! Oh..."

It was at this moment that both the eyes of the draconequus and the ram had met. Locked into each other's gazes, one had contempt, the other filled with fear.

"Uh, Discord? Please tell me this is all a big joke?" Rainbow asked, hoping to be rhetorical.

"This is no joke," answered Grogar confidently, "I, Grogar, Father of Monsters and soon-to-be Emperor, have returned!"

The heroes gasped, stunned by the revelation that the one and only sorcerer Grogar has returned from the unknown he was banished to. Fluttershy, still hurt from the impact, slowly got up. She too, gasped when she saw both Grogar and Discord at the same place, at the same time. Realisation immediately hit her.

"Is that?" the yellow pegasus asked.

"Fluttershy, I need you to immediately fly as far and as fast as you can to Ponyville. Keep the children and citizens safe, especially your animal friends," requested Twilight, grim and serious.

Fluttershy saluted to the princess and immediately took off to Ponyville, heeding her orders and promising not to let her down.

Chrysalis hissed and snarled at Fluttershy flying away and was about to give chase until Grogar stopped her.

"Leave her, all the pieces have fallen into place. Do not screw this up," said Grogar as Chrysalis nodded in affirmation.

"Fizzlepop, Flash, go and rally the guards, Star Swirl, tell Stygian to send a message to my brother and sister-in-law to launch a call-to-arms, the rest of you, stand by me, we're in for a fight of our lives," Twilight continued.

Upon hearing Tempest's real name, the villains did a spit take and laughed very hard.

"Fizzlepop? Seriously?" Chrysalis asked in amusement.

"As if pony names couldn't get more ridiculous!" added Tirek.

"Ugh, after this, I want a name change, remind me to book an appointment with Mayor Mare. Flash, with me," commanded Tempest.

"Aye, aye, captain," saluted Flash as both he and Tempest retreated to the Canterlot castle.

Star Swirl nodded, before finding a safe spot to relay the urgent message.

Both the Mane Five plus Spike and the villains stand off against each other. Tirek and Grogar cricked their knuckles and neck respectively. The heroes assumed their battle stance. Both stared down at one another for what seemed like an eternity before one of them broke the silence.

"So these are Equestria's champions? They don't seem to live up to Gusty and her cohorts," taunted Grogar.

"Gusty was a great mare! And we'll try not to disappoint," declared Twilight.

"You may have many allies, but I'll say this is fairly even," grinned the ram.

"Oh yeah?! You and what army?" asked Rainbow Dash.

"Why don't you take a look around yourself?" answered Grogar to the rainbow-maned mare.

As if on cue, bony, skeletal arms popped up from the ground. The arms belonging to Grogar's undead army then try to push themselves out from the underground, carrying their weapons with them before proceeding to surround Twilight and friends.

"You just have to say it, do you?" said Spike, who was unamused.

"Oh, uh, no matter, we can handle a pile of bones, right gals?" asked Rainbow Dash who blushed at the slight miscalculation.

"Rainbow Dash, this is more than 'a pile of bones', whose to say there aren't more?" retorted Applejack, who's as unamused as Spike was.

Twilight took a deep breath, before proclaiming, "Well? Do your worst, come and get some."

"We will, get them," ordered Grogar calmly as the battle commence.