It's been awhile and in honor of the Injustice 2.I have rewritten my original written plot and added a storyline for the sequel plot. I will repost the first one and then the one for Injustice 2, or rather Disharmony 2.

DISHARMONY





Prologue…

Many years after the events of the series, Alicorn Princess Twilight Sparkle wakes up one morning, and senses something strange, two heartbeats coming from one Pony, Herself. She is pregnant. Excited by the news, She begins to rapidly blur out details concerning how to raise their child which seem to plan out their entire life including: naming it Nyx if it's a boy, moving to Ponyville because Canterlot is too big, flying lessons from Rainbow Dash if they have wings and then proceeds to go on a tangent wondering if Alicorns can be naturally born. Her husband( possibly Flash Sentry) slowly wakes up, smiles and throws a book at Twilight. It hits her and gets her attention. " Did you just throw a book at me?" she asks. He calms her down and they agree to take it slow. Afterwards, Twilight runs to tell Celestia, but finds Luna raising the sun in her sister's place to her disappointment. Celestia is off on a diplomatic mission.





AppleJack shows up in Canterlot, Twilight has not seen her in quite some time, and they chat, until Twilight realizes that Applejack wouldn't have come to her for a casual visit, after so much time. AJ reveals that their friends have all fallen on hard times. Granny Smith passed away and the Apple Farm has went under. Fluttershy's house was destroyed and she is forced to live in the forest because no one will take in all her animals. Pinkie Pie has diabetes from eating too much sweets. Rainbow Dash broke her wing and was kicked out of the wonderbolts, and Rarity's home was vandalized. Upon hearing this Twilight vows to take care of her friends, she quickly solves all their problems, the last one being AJ, who she convinces to sign a contract making Apple Acres property of the government, as such it will be kept financially stable so long as Twilight allows. AJ and Rainbow Dash tell Twilight about recent "incidents" around Ponyville that seem to be tied to Discord such as cotton candy clouds and chocolate milk rain, though Twilight trusts Celestia and Fluttershy’s belief that he has truly changed.





Twilight and Applejack return to Sweet Apple Acres, revealing that she is getting worried about Celestia's continued absence, and to make matters worse, both Discord and the elements have vanished as well. They gather the others, who head to Canterlot. Discord appears to make his move and fights Twilight, during which she senses herself miscarry, and becomes so angered she appears to kill Discord by impaling him with her horn, only for the illusion to fade and reveal that Twilight has killed Celestia. She screams and repeats that she is so sorry but Celestia tells he it’s alright.She knows she didn’t mean to, before she dies. Twilight cradles he mentors body and cries. Discord teleports in and taunts her. Twilight becomes enraged and summons powerful dark magic,which encases Discord in stone.She then mentally shatters Discord’s statue form into pieces.Discord’s head falls to the ground and breaks into a million pieces.





Elsewhere…

The Mane Six( including a unicorn Twilight) are chasing after Discord, just as they are about to defeat him with the elements, they all vanish in a flash. They find themselves in a strange different Ponyville, without AppleJack. The other mane six split up to check on their respective homes.





CHAPTER ONE:FLUTTERSHY

Fluttershy makes it back to her cottage to see evil armored versions of Zecora and Gilda beating Trixie. She just barely fights them off( in case you're wondering, Fluttershy is being protected by her animal friends, who do the actual fighting). Trixie then leaves. Fluttershy hears Pinkie and Rarity being attacked and finds their attacker is an evil Iron Will, who reveals that in this world Fluttershy is his top apprentice. Fueled by her desire to save her friends, Fluttershy musters up enough courage to fight and defeat him. She is then faced with an evil Fluttershy( evil Fluttershy: You're going to FEAR ME!!) she defeats her counterpart( Pinkie: All that yellow’s not good on the eyes). Fluttershy, Pinkie and Rarity leave and are confronted by what appears to be AppleJack.





CHAPTER TWO: TWILIGHT SPARKLE

Twilight arrives at the library, which is now much larger, and available to the public. She learns from a librarian the alternate world's history: after Celestia's death Twilight took over as ruler of Equestria. She suddenly meets with two of the evil Twilight's generals, one of which is the evil universe Rainbow Dash( wearing the shadowbolt costume) and a Shadowbolt Derpy Hooves. They mistake her for her counterpart( though they are confused as to why she doesn't have wings) and hand her a piece treaty signed by Shining Armor and Cadance, that turns the Crystal Empire over to Sombra, Twilight fights them and then the alternate Shining and Cadance, who were about to agree to it. Shining sends guards against Twilight but, she is saved by Discord, who reveals that the evil Twilight allowed anyone to join her armies, including her still grateful for helping them friends, and villains like Chrysallis, Sombra, and Nightmare Moon( Luna). Discord teleports Twilight to her friends, where they meet the alternate AppleJack. Alternate AppleJack( which we will refer to as AJ) is the only mane six member fighting the evil Twilight, all others have joined her, save for Pinkie Pie who was killed by her.





AJ provides them with a serum Twilight created that grants them power to rival alicorns, which Twilight uses on her minions and which AJ stole( a modified version of the serum from " Double Rainboom", minus the side effects). AJ reveals her ally: Sunset Shimmer! Sunset explains that in this universe, she did not stop being Celestia's student, and studied alongside Twilight, thus being the first friend she ever had. That night, Twilight meets with another ally: Trixie, who discards her wizard hat and cape, and accepts the others as her friends with Twilight's support( it's only a Twixie fanfic if you imagine it to be). In Canterlot, Alicorn Twilight is standing in front of an unseen but, massive beast, Evil Rarity is putting a dress on her, while Alicorn Twilight seems to be attempting to control the beast. The beast snarls at Rarity, and Twilight jokes that she thinks " he likes you". Evil Fluttershy comes in and tells about her encounter with the "duplicates"





AJ's plan was to bring the other elements into her world using Sunset Shimmer's magical powers, so they may find the Elements and use them on Alicorn Twilight, she made the spell so AppleJack would not be sent with them as they don't need her. Unfortunately, the Elements are still missing from before Discord's death and no pony knows where they are, The mane six decide to track down the Discord of their universe.





CHAPTER THREE: DISCORD

Discord is found and attacked by The Applejack of his universe, who he defeats but then leaves imprisoned just as Twilight's forces arrive and arrest her. Discord is then found by Pinkie Pie, who wandered off from the group. They fight and Discord decides to create Pinkamena using Pinkie. She fights the clone but the two then become friends and run off to harass Twilight's forces including Discord having to fight the evil Fluttershy. The mane six arrive with AJ and join forces with Discord and Pinkamena. Discord tells them a riddle similar to the one from his first appearance, that hints at the element's location. Twilight deduces that from the part about "beginnings". Discord means the castle in the ever free forest where the Mane Six's first adventure began.





CHAPTER FOUR: PINKIE PIE

They are forced to pass through the ruins of Apple Acres, which Alicorn Twilight shut down after AJ went rogue via their contract. They fend off a corrupted Big Mac, still living in the ruins and a corrupted Maud Pie, before making it to the forest. They find the elements but, are attacked by Nightmare Moon and Sombra, who almost destroy the elements but, Twilight saves them before the group makes a hasty retreat.





CHAPTER FIVE: SPIKE

Back in the mainstream Canterlot, the Princesses have discovered the location of the mane six, via a mirror like the one from Equestria girls, Spike is with them,and he hears Twilight through the portal and jumps through. He overhears Sunset and Trixie discussing a plan to kill Twilight, and attacks them before the misunderstanding is cleared up. They then hear Alicorn Twilight announce that Applejack has been caught and will be executed, revealing that the Main AppleJack has been caught and will be hanged. They decide to save her.





Twilight sends Spike to the Library to steal a book of spells only he and Twilight know about, and thus the Alicorn Twilight would be caught off guard by what it contains. Spike is surprised by the evil Rarity flirting with him before she is knocked out by Trixie, who lets Spike in on Her and Sunset's plan. Spike retrieves the book, a book of classified files on equestria, including first contact with humans several generations ago, the origin of the three races, files on Doctor whooves and a conspiracy involving the rainbow factory.





CHAPTER SIX: RAINBOW DASH

The factory is discovered to have been turned into a base where Twilight's empire culls the weak. They send Rainbow Dash there to set the Factory's boilers to explode, with instructions from Twilight's book. This was meant as a method to destroy all evidence of the factory's doings when they used to be secret, the resulting explosion will be devastating. Dash goes to the factory, and impersonates herself. However, she blows her cover when the factory staff attempt to force her to kill Scootaloo, who was sent to the factory(without a cutie Mark). Dash battles her counterpart and Derpy Hooves and rescues Scootaloo.





CHAPTER SEVEN: TRIXIE

Trickier sneaks in and sets the factory boiler to expose while Dash distracts them but fights Fluttershy, Rarity,Derpy and Rainbow Dash while escaping.





CHAPTER EIGHT: APPLEJACK

The group then attempt to save appleJack from execution in Canterlot, Applejack is rescued by AJ and Pinkie Pie, with help from the older cutie mark crusaders( including an AppleBloom who is an expert mechanic). The Rainbow factory explosion masks their escape,with a massive rainboom explosion.





CHAPTER NINE:SUNSET SHIMMER

Sunset enters the battle and defeats many foes including a betrayal by Discord and Pinkamena and a fight with the evil Rainbow Dash. The mane six attempt to use the elements of Harmony against Alicorn Twilight but, Sunset fights and knocks out Twilight,and Trixie takes her place as the element of Magic, causing the elements to fail. Sunset then steals the element of Magic, intent on killing Alicorn Twilight personally out of envy for her becoming an alicorn despite Sunset being Celestia's student longer, and is about to use the element on Alicorn Twilight, when she is attacked by evil Rainbow Dash, causing the element of Magic to shatter, rendering all of them useless. Alicorn Twilight strangles her while shouting about how Sunset betrayed their friendship. Sunset's last words to Alicorn Twilight are: "friendship is pathetic" before dying. Alicorn Twilight sees everyone horrified of her actions, then angrily screams and flies off.





CHAPTER TEN: LUNA

At a later meeting she reveals her plan to destroy Ponyville, and Canterlot, and then invade the main universe. Cadance protests and is killed. This convinces Luna to switch sides. She tries and convince Shining Armor to do the same but he attacks her, far too corrupted. Luna also fights Rainbow Dash,Big Mac and then escapes, fighting Pinkie Pie when she arrives at the base of the Mane Six. Luna reveals their plan. Just then cloister bells are heard, the Tardis shows up with Doctor Whooves and Derpy. The princesses contacted them, and the Doctor agreed to attempt intedemensional travel with the Tardis to rescue the mane six. AJ wants the mane six and spike to go back to their world with the Doctor but, they see Ponyville being destroyed in the distance and decide to stay and help. The mane six suggest giving the serum to Twilight, which would boost her power to powerful levels. AJ refuses, believing Twilight would be consumed by her lust for power.





CHAPTER ELEVEN:RARITY

They are then attacked, during which Discord appears again and transports Rainbow dash to clouds dale where the evil rainbow Dash is about to lead the Pegasi to destroy Canterlot, Both Dashes then begin fighting. Rarity fights off several of Twilight's forces.





Meanwhile, AJ and AppleJack get into a fight over giving Twilight using the serum, while the other mane six except Twilight fight their counterparts. The originals win and Twilight transforms into an Alicorn from the serum while Dashie gives a passionate speech to the Pegasi convincing them to help them.





CHAPTER TWELVE RINCESS TWILIGHT SPARKLE

good Alicorn Twilight travels to Canterlot, first defeating Sombra by freezing him in Crystal, and then confronting Chrisallis and the changeling army. Chrysallis: are you ready to take on the might of the changelings, Twilight: yes,WE are!. Dashie shows up with the pegasi and a massive battle begins and ends with Twilight defeating chrysalis and the changelings retreating, seeing this, Alicorn Twilight releases her secret weapon, which is revealed to be the alternate universe Spike, now a fully grown, savage, blood thirsty Dragon.full grown Spike attacks Twilight and is eventually defeated. Both Twilights then meet for the first time and briefly argue

Evil Twi: I'm going to kill you and bring you're Celestia to my universe, and when she sees what I've done she'll be…

Good Twi: She'll be afraid and disgusted!

Evil Twi: but, she'll be alive!





The two fight and the battle ends in a massive clash.

Evil Twi: I'm saving the world!

good Twi: I'm saving the world from you!





They clash and the noble Twilight emerges victorious. The evil Twilight is taken away and the serum's effects wear off. The mane six help to restore order, and finally prepare to go home. AJ and Twilight are having one final conversation about the " what if " possibilities, and Twilights fear she may become as twisted as her counterpart, Aj reassures her as they walk away. The camera pans and we see Alicorn Twilight has been turned to stone, standing on the podium Discord's statue once stood on. It then the begins to crack, with a bright light shining through the opening.





The end?

(The song "assembled we are strong" plays over the credits")