All the Pretty Little Horses
Part 1: At the Gala
Ten... Years... Later...
Equestria has been split fully into thirds; Canterlot, Greater Equestria, and the Crystal Empire. The three kingdoms exist peacefully enough so that the Windigoes stay away, but there are enough underlying tensions that no one is completely at ease. The Grand Galloping Gala has become an annual event used as a summit for the monarchs of the three kingdoms to meet and discuss things.
Fancy Pants and Fleur De Lis are attending the latest Gala when they run into an old friend; Rarity. The unicorn reintroduces the pair to her husband, Crescendo, and through their conversation we learn a great deal about what has occurred over the last decade in the personal lives of Ponyville’s residents;
-Lyra served as mayor for two terms once Applejack “ascended,” but has now quietly retired to live with Bon Bon and the Cake Twins.
-Diamond Tiara ran for Mayor but dropped out of the race after continued harassment for the actions of her father. She left Ponyville and no one has seen her since.
-Caramel is the current mayor of Ponyville.
-Rarity and Crescendo are high ranking members of Applejack’s court and have a young daughter named Ruby.
-Applejack, the Terra Queen, has married Rainbow Dash. Due to the pressures of ruling, they have no children of their own.
-Sweetie Belle married Button Mash, but he was tragically killed in an event all attending refer to only as the "incident." Sweetie has found salvation in life through her musical tours, the latest stop being the Crystal Empire.
-Fluttershy has become the defacto matriarch of the Apple family, with Scarlet being Applejack's hoof chosen heir to the Terra Throne.
Their conversation is cut off by the official introduction of the monarchs and a brief musical performance by a returning Sweetie Belle. Following the show, Sweetie Belle finds Applejack and asks to speak to her privately. The true nature of her trip to the Empire is revealed; a recon mission to explore the Empire's food supply levels. Applejack is grimly pleased to hear that the Empire is struggling with food stores, something she knows she can use in future negotiations. Sweetie Belle also reveals that she has fallen for her crystal pony escort Obsidian and that he wishes to defect to Greater Equestria to be with her. Applejack takes it under advisement and seeks out Luna.
Applejack and Luna have become secret confidantes dead-set on re-unifying Equestria under a new democratic system of government. Applejack tells her what she's learned about the Empire. Luna suggests that the only way for a speedy reunification is to remove Cadance. Applejack, still haunted by her actions in the execution of Blueblood, refuses.
Celestia finds Glorious Hope sulking in her room. The young changeling queen has entered a moody teen phase and now insists on going by the name Masque. Celestia finally convinces her to join the party by telling her that Morning Dew is there.
Back at the Gala proper, Moon Shadow and Morning Dew each ask Scarlet to dance. After a few playful barbs between the three, Scarlet chooses to dance with Moon Shadow. Morning Dew sulks until Masque appears and convinces him to dance with her. The three monarchs watch this play out, each planning different things involving the youngsters.
Applejack, Celestia, and Cadance gather for their summit in another chamber. Applejack presses Cadance about the Empire's food stores, but Cadance refuses to admit there's an issue. Celestia plays mediator, eventually securing more food for the Empire in exchange for further relaxing of their stringent travel visas.
Outside the chamber, Obsidian is approached by Luna's student Starlight Glimmer. She gives him a gift; a locket she says is from Applejack as a token of welcome to Greater Equestria.
Later that night, Luna visits her son in his room. He confesses that he's fallen in love with Scarlet. Luna is terrified, knowing that Cadance has been trying to arrange a marriage between Morning Dew and Scarlet (a vital piece of Luna and Applejack's reunification plan.) Seeing no other option available, Luna visits Cadance's chambers and strikes a bargain. The two of them will have a duel, single combat. Should Luna win, Cadance will cede her throne to Morning Dew. Should Cadance win, Luna will voluntarily reseal herself in the moon, just as Cadance originally demanded.
The widows of Shining Armor square off in the castle courtyard. The sheer magical force of their fight wakes everyone in the castle and they run out to watch. By tapping into her deepest reserves of magic, Cadance accidentally lets her disguise slip and reveals her twisted and terrifying new form as the Crystal Empress. She gains the upper hoof and mocks Luna, telling her that it is no longer her banishment she seeks.
It is her death... and the death of her son.
Luna loses control and becomes Nightmare Moon once again, easily throwing down the Empress and demanding she yield or die. Moon Shadow cries out for his mother, breaking her concentration long enough for the Empress to stab her through the throat with her horn. The Empress escapes in the ensuing chaos, guarded by Flash Sentry and Obsidian, but Morning Dew is captured by Starlight Glimmer. Obsidian promises Sweetie Belle he will return. Celestia and Moon Shadow rush to Luna and comfort her as she dies. Applejack leaves to take Scarlet home to Ponyville.
As the sun rises, Celestia watches over Luna's body. She recalls Discord's words that they would leave this world together and advises her sister to wait for her.
Cadance returns to the Empire with Flash Sentry and Obsidian in tow. She celebrates Luna’s death and displays her prize, the real reason she agreed to the duel in the first place; the Apple of Chaos, stolen from Celestia’s chambers by Flash Sentry during the fight. She reads Obsidian's heart and discovers his intent to defect. She attacks him... and sees the locket. She inspects it closely until she sees Luna's sadly smiling face in the reflection. The locket opens, releasing a magical blast that kills Cadance, Flash, and Obsidian. The Crystal Throne shatters.
Part 2- The Price of Peace
A week after the dual tragedies, Celestia summons Morning Dew and tells him an investigation has found no further threats in the Empire and that he will be returning there to assume the throne. Morning Dew is still shaken by everything, and Celestia offers warmth and advice that he appreciates. She draws from him a tentative promise to reunify the Empire with Canterlot in the near future and he departs after uneasy goodbyes to Moon Shadow and Masque.
Applejack, Rarity, Fluttershy, and Rainbow Dash discuss the recent developments. AJ believes that it's time to attempt democracy again, but Rarity reminds her of the disaster that happened last time she tried. (the previously mentioned “incident.”) They receive a message from Celestia requesting their presence in Canterlot.
In Canterlot, Celestia lays out her plan; Morning Dew ascends to the Crystal Throne, Moon Shadow takes Luna’s place, she abdicates her throne to Masque, and Applejack abdicates to Scarlet. With the new quartet in place, the monarchs reunify Equestria as a whole and rule together. Applejack is against the idea, fearing that all her work toward democracy will be undone. She and Celestia argue, and in an attempt to quell the argument, Starlight reveals Luna’s last act in assassinating Cadance. The assembled ponies' shock is put aside when a tremendous flash fills the room.
When the light clears, Twilight Sparkle is there... along with Pinkie Pie.
In Ponyville, Time Turner's wedded bliss with Derpy is shattered when there's a knock on the door. He opens it to find his old friends from the Guild of Time Defense; Colgate, Nevermore, the Tall Pony, Pipsqueak, and... himself. Well, himself as a pegasus.
Colgate explains that she ensnared some of Turner's temporal essence when he left the Guild and used it to create a facsimile of Turner's old self so that part of him could remain in the team. Turner is furious, though Derpy seems intrigued at the possibilities. ("Two of them? My goodness." She said, fanning herself with a hoof. "Is it my birthday?") Colgate explains that they are within two years of the end of the timeline, and thus must see the flow of time through normally as there are too many variables to perfectly pinpoint the moment the timeline dies.
Back in Canterlot, Twilight has just finished explaining all of this to the others. The girls share a heart-felt reunion with Pinkie, and the true nature of her "death" is finally revealed; the real Pinkie was actually sealed away in the Mirror Pool by accident. To correct this imbalance, the last remaining clone was magically linked to the original, gaining her memories and full personality. Now understanding her true nature and her shortened life span (magically generated clones tend to break down more quickly) "Pinkie" sought to live life to the fullest, hence her hastened courtship and marriage to Caramel. When she died, the original Pinkie was finally freed from the pond and snatched away by the Guild.
The joyous reunion of the Mane 6 quickly sours. Applejack and Rarity are still bitter at Twilight for leaving them high and dry during the Battle of Ponyville and the ensuing occupation. Dash is adamant that her depression and alcoholism could have been averted if she had just known Pinkie was still alive. Fluttershy refuses to allow her daughter to be used as a pawn in Celestia and Applejack’s games. The argument reaches a breaking point and the friends split apart. AJ and Dash remain in Canterlot to await Morning Dew's return. Fluttershy returns to Ponyville with Rarity, Pinkie, and Twilight to see everyone... and so she can speak to Scarlet.
In the Crystal Empire, a still reeling Morning Dew is wandering the palace when he meets the mysterious old maid. She tells him not to worry, as his mother left instructions for her to help him should anything happen to her. She drops her magical disguise and reveals herself as Sunset Shimmer, Celestia's former student who fled into the Mirror when her loyalty to Tirek was revealed. She explains that she and Cadance had been planning on building an army to seize all of Equestria before Starswirl sealed the portal. She hints that other plans were in the works, but Morning Dew doesn't want any part of it. He wants peace. Shimmer scoffs and casually reveals that he's been lied to all his life; Moon Shadow is his brother, not his cousin. Morning Dew is shaken, but he stands fast. He tells Shimmer to pack her things, as she'll be leaving the Empire upon his return from Canterlot.
In Ponyville, the Guild go to visit the “Catalyst,” a pony that essentially remains the same in every timeline that acts as a sort of organic repository of each timeline's history. The Catalyst is revealed to be Bon Bon Heartstrings. After confirming that her wife still loves her no matter what she is in any reality, Bon Bon allows herself to be activated. The Guild questions her and confirms how each of their alterations have shaped the path of things to come. Just before they finish, Nevermore asks for the identity of the Harbinger. The Catalyst cannot see as there are two possibilities. Only three things are known; she is a mare, she is a unicorn, and she has known great loss. The Guild is split. Half believe the Harbinger to be their own new recruit Dinky Hooves. The others believe her to be Sweetie Belle.
Mayor Caramel has a reunion with Pinkie Pie. Things are tense between them until she tells him she shared in all the feelings her clone did, including her deep love for him. Caramel uses his mayoral powers to reinstate their marriage at once.
Twilight has a moment at Spike’s grave, apologizing for not being there for him. She is found by Rarity, and the two finally make peace.
Fluttershy finds Scarlet tending to her orchard and the two reflect on their haven of peace and serenity. She reluctantly lays out Celestia's plan. Scarlet confesses that she has feelings for Moon Shadow and agrees to the plan. She assures her mother that the price for peace is almost never too high. As she leaves to pack, Fluttershy weeps with pride at how her little one has grown.
As Morning Dew arrives in Canterlot, AJ and Dash reflect on their struggles over the last decade. Noting AJ's reluctance to abandon her quest for democracy, Dash reminds her that now they'll finally be able to start their own family. AJ finds some solace in this, and in the assurance that her niece will not stop fighting her aunt's fight for her.
All parties finally reconvene in Canterlot. Celestia explains her plan to Morning Dew, and he accepts. As the new treaties are formalized. Morning Dew proposes to Scarlet, but she rebuffs him for Moon Shadow. Furious, Morning Dew refuses to sign unless Scarlet marries him. When all parties ultimately refuse, he leaves in a rage. Masque watches him go, her heart broken.
Returning to the Crystal Empire, Morning Dew finds Sunset once again and asks her about his mother's plans. She reveals a secret lab being manned by Gadget (it's mentioned in a previous scene that he vanished after the "incident" in Ponyville took the life of his mother). Gadget reveals that he's been using the captured Apple of Chaos to create a new kind of weapon; the Elements of Discord;
Magic = Skepticism
Loyalty = Betrayal
Laughter = Sorrow
Honesty = Lies
Kindness = Cruelty
Generosity = Avarice
The Elements are nearly ready and only need Bearers to activate them. Gadget takes the Element of Skepticism for himself, citing his loss of belief in Applejack. Spitfire reveals herself as Gadget's lover and claims the Element of Betrayal, citing Soarin's actions in 'On Swift Wings.' Sunset Shimmer herself takes the Element of Lies, citing her mastery of manipulating the truth. Morning Dew finds himself drawn to the Element of Avarice, but holds himself back. Unable to make his decision, he flees. Sunset assures Gadget that he'll come around, and reveals that she's sent invitations to candidates for the last two Elements.
In Canterlot, Moon Shadow feels guilty about the situation. Now that he has his mother’s throne, he decides to act without Celestia's approval and dream-walks into the minds of the sleeping Crystal Ponies. He attempts to plant the idea that they should convince his brother to do the right thing and unify, but finds he is inexperienced in dealing with so many dreams at once. He loses control, infecting many Crystal Ponies with nightmares so severe that they die from fright.
When the events are relayed to him the next day, Morning Dew knows what must be done. He returns to the lab and claims the Element of Avarice without hesitation. The last two candidates arrive; Maud Pie and Diamond Tiara. Maud, broken emotionally and still believing Pinkie dead, accepts the Element of Sorrow. Diamond Tiara, after enduring years of abuse and hate for something she had no part of, decides she will be the monster they want her to be and takes the Element of Cruelty. The Bearers found, the Elements activate.
In Canterlot, a message arrives with news that shakes all to their core; the Crystal Empire has declared war on Greater Equestria and Canterlot. To make matters worse, Masque has vanished.
A terrified Moon Shadow explains what happened, and is lambasted by Applejack. She lays all of the blame on him and throws him to the ground, demanding his surrender. Traumatized, Moon Shadow does so and is locked in the dungeons. Citing Masque’s disappearance, Applejack ascends and officially takes the thrones of Canterlot. She reunifies it with Greater Equestria and orders the military mustered. If Morning Dew wants a war, he'll get one.
In a direct mirror of their conversation all the way back in 'Apple Family Secrets,' Celestia notes the tragic irony that Applejack has finally answered the call in her blood. She pledges to help however she can, and bows to the new Queen of Equestria.
In a brief interlude, we see the "incident" that occurred in the time-skip; a confrontation between Crystal Empire sympathizers and Canterlot loyalists during a pro-democracy rally in Ponyville that somehow led to a massive explosion that killed many ponies, including Gadget's mother Sour Grapes and Button Mash.
Part 3- This Endless Waltz
Nearly two years later, the war still rages. Even with aid arriving from Scootaloo and the Children of the Hurricane, the Crystal Army continues to gain ground now that the Elements of Discord have been loosed on the field, their Bearers fully trained. The Guild is getting nervous, as they know the prophesied final battle is approaching rapidly. No one has seen or heard from Masque since the war began, and Moon Shadow is confined to Canterlot Castle’s dungeons, his visits from Scarlet the only reprieve from his misery.
Celestia tricks the Mane 6 into gathering in Canterlot and tells them they must figure out why the Elements of Harmony have yet to reactivate. Each confirms that they've stayed true to their chosen value, save Applejack. At her friend's urging, AJ finally breaks down and confesses her sins and lies. She admits that while she does want democracy over monarchy, she loves being the Terra Queen and wouldn’t trade who she really is for anything. Now that she’s finally honest with herself, the Elements of Harmony reawaken. And just in time, too; word comes that the last defenses have fallen and the Crystal Army is marching on Canterlot.
Applejack releases Moon Shadow from prison and swears to him that if he fights with them, he can marry Scarlet.
The armies come face to face on a great field. The Elements of Harmony and the Elements of Chaos stand before one another. Maud refuses to believe that Pinkie is alive despite her sister’s being there, insisting it’s a trick. Celestia tries to convince Morning Dew that Sunset is only using him to free her master, but he doesn’t listen. Everything comes to a standstill as Cadance’s spirit shockingly appears, begging her son to stand down. Morning Dew appears to consider… until Sunset rips away the disguise.
It’s Masque, who has spent the whole war in the Empire in different disguises trying to get Morning Dew to stop the war.
Morning Dew decries the deception, but says that he will spare Canterlot if his brother is delivered to him and Scarlet becomes his wife. Scarlet lashes out at him, calling him a spoiled child. He attacks her in his anger, but Moon Shadow takes the hit. Instead of dying, new magic floods through him and he somehow becomes a new version of Nightmare Moon, complete with a magical pair of wings. The brothers collide at last, and the armies follow suit.
Just as they did before years ago, the Guild of Time Defense looks on from a mountain top… waiting.
The ambient magic of the dueling alicorns gives Rainbow Dash her wings back, and she engages in a brilliant aerial duel with Spitfire. She finally defeats her former idol by tricking the mare into a suicide dive straight into Gadget’s huge war machine, killing them both. Dash barely escapes the explosion.
Maud and Pinkie face off, but Pinkie refuses to fight her sister. Her pleas for Maud to see that she’s the real her finally gets through, and Maud collapses into Pinkie’s embrace, weeping.
Applejack battles the now borderline insane Diamond Tiara, apologizing for all the misery she endured. The mad-mare refuses to back down, but her final attack on a wounded Applejack is cut off by Fluttershy. Fluttershy’s unrelenting kindness finally gets through, and Diamond Tiara throws away her element and surrenders.
Sunset dispatches Starlight before turning to finish Celestia. The princess, however, has had enough and at last gives in to the darkness inside herself. The Phoenix Queen rises once again, incinerating Sunset and casting both Sons of Armor down. The power is too much for her aged body, however, and Celestia’s heart finally gives out. She dies in Twilight’s arms. As Moon Shadow and Morning Dew move to finish their fight, Twilight finally has enough. She explodes with power, transforming into a new being; the Twilight of the Gods.
Not missing a beat, the Guild of Time Defense freezes the moment in time before Twilight’s power can destroy the timeline. As expected, the beast from before appears. As the Guild gets ready to finish the fight, they are betrayed… by the Tall Pony.
And Nevermore.
As Nevermore’s magic holds them hostage, the Tall Pony finally lays everything out; he has been helping the beast eliminate timelines so that he can feed on the raw energy himself. This unorthodox diet has changed him, made him less of a pony and more into something new. He reveals that Nevermore is the Emissary of Shadows, the entity acting as a split personality to aid the forces of evil undetected. Nevermore begs for forgiveness, now fully unable to control his own body. Those assembled watch as the beast finally manifests and is revealed at last; King Sombra.
As it turned out, N’er Do Well’s essence escaped from his prison and found footholds throughout the timelines. One of those footholds was in King Sombra. While the Tall Pony has been acting out of hunger, Sombra has been manipulating timelines to create one perfectly suited to his purposes; one full of alicorns to give him enough power to attain godhood, and also holds the last key to his total conquest of all reality.
He needs a Harbinger. And he needs one formed of his own blood.
Sweetie Belle is the Harbinger.
Nevermore uses the last of his will to free the Guild. As the Emissary takes hold, he begs Time Turner to kill him. Turner refuses, but his doppelganger moves to do it for him. A good thing too, as it was a trap. The Emissary self-terminates, taking Doctor Whooves with him.
Colgate stops the Tall Pony from killing Pipsqueak and fights him. She magically brushes his face out of existence, and he flees into the darkness to torment some other timeline…
Dinky Hooves frees Sweetie Belle from the frozen moment and tells her that only she can fix this. Only she can walk through and alter timelines. Applejack is also unfrozen (a single hair on her coat was touching Sweetie Belle’s when the moment was frozen) and she tries to help the Guild. Sweetie realizes what she has to do and begins gathering magic. Sombra moves to possess her, but Applejack holds him back just long enough for her to say the magic words;
“No more alicorns.”
The timeline is altered, transforming all alicorns into unicorns. With no alicorns to draw magic from, Sombra is weakened enough for the Guild to strike the final blow.
The moment is unfrozen, and all present watch as Applejack collapses. She has been mortally wounded by Sombra, but she dies with a smile on her face. Held by the mare she loves, surrounded by her friends…
She dies, but Equestria has been saved.
For all time, it has been saved.
Epilogue- The Old Gray Mare
One hundred years later…
Rarity is again at the Grand Galloping Gala, this time as the guest of honor. The elderly mare is the last of the Mane 6 still breathing. She reflects on the peace and prosperity the united Equestria has experienced over the last century. Equestria is now a democratic republic, just as Applejack dreamed. The quartet of Moon Shadow, Morning Dew, Scarlet Apple, and Glorious Hope remained as figureheads for the brave new land Equestria has become until they were no longer necessary. Ponies have married, had children, and died. Time has moved on.
Now only she remains.
She wanders onto the grounds of Canterlot Castle and finds herself in the statue garden. She lays down beside the statue of Golden Haze and considers taking a nap.
Imagine her surprise when Captain Haze leans down and offers her a hoof.
She rises, not shocked at how young she feels now. She lets Haze guide her back inside and finds the grand hall filled with all the ponies lost along the way.
There are the Apples, all together and smiling.
Here are the Cakes, beaming at Lyra and Bon Bon for how well they raised the twins.
Here is Crescendo, who gives her a kiss before stepping aside.
And there, at the center of the room, stands a purple drake with his back to her. He turns, and he smiles.
“Rarity?”
THE END
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Huh, so Sweetie is like the Scarlet Witch? I didn't know she was that powerful.
Definitely an interesting conclusion to the story, lots of next-gen players, though the Mane 6 still play a final, crucial role. Still to dark and brutal for my liking, but I'm sure others would have enjoyed it.
This is actually my first time commenting on this site (I'm usually one of those ninja type watchers that'll give the story a like and favourite and be too shy to comment lol) but I've actually been following for you for a really long time now and need to comment to this! THANK YOU for the wonderful journey with this story!! Don't be sad or beat yourself up that it didn't work out, you still gave an ending and that's what matters! It needs to be a story that you enjoy writing and sometimes, it just happens with projects. Otherwise, the wait was totally worth it and even though it has ended with the synopsis, you still wrote even that beautifully! So, thank you!!! <3
Much applause to you!! 
I remember back when I first came on this site, the first story I read of yours was phases of the moon and I loved it but stupidly read it out of sequence, haha. When I realised it was a sequel and not only that, part of a whole continuity (and read it and followed it all in order!), it was really exciting to occasionally reread through all your stories whenever a new one would pop up. I would try and find pieces of the puzzle I may have missed or just get back into the whole universe you created. The suspense would even leave me dreaming of the conclusion at times!
It's been an epic ride for sure! 
I also love the drama and just how dark and real it gets, not just here but throughout the whole thing. I notice some people here aren't too keen on that part but in all honesty, I love it and think it suits your writing too.
Also, when you say you 'couldn't think of a better curtain call to seal everything up', does this mean you had different plans for the ending originally? I might be misreading that, but I would be curious to hear if you did!
Another question is I understand from a journal I read of yours that 'Dear Sweetie Bell' was written based from an experience, but was wondering if you were inspired by any other stories or authors with some of the other parts? Or just some other stories which are similar to your writing (or in specific similar to this continuity) you could recommend?
Again, you're a great writer and you have always been one of my favourites and an inspiration! I have also enjoyed your other stories too, so I wish you all the best for your future/current projects, and life in general! I'll probably be one of the quiet ones lingering around, but for sure will continue to read, support and recommend your works to people online!
2 doctors includes 2 "d"s derpy's about to get bucked i n all the right ways lol