Empire of Darkness

by Timeman202

Rating: mature
Tags: Romance, Shadowbolts, King Sombra, Cutie Mark Crusaders, Suicide / Self Harm, Violence, Death, Twilight Sparkle, Main 6, Drama, My Little Pony: Friendship is Magic, Dark, Alternate Universe
Length: 8452

Things turn out differently at the Tree of Harmony for the Main Six

After Sombra destroys the Tree of Harmony and brainwashes the Main 6, Spike runs off and tries to get help. Unfortunately for the young dragon, he really should not have underestimated the self proclaimed King of Shadows and his plans.

Notice: This was a request made by chazkopa - Fimfiction and is also a bad ending fic. If you clicked on this title expecting things to turn out great for the good guys, then I'm sorry but your good ending is in another fanfic. I would still appreciate feedback as I make this, and who knows; I may eventually add more to this after I finish the main request that Chazkopa asked for. Also, I am adding in Twibra romance into this story because King Sombra x Twilight Sparkle is amongst the ships in "Ships I will Write about". It's also why I am making the executive decision to not include Flash Sentry into this fan-fic so I'm not tempted. As I've said many times, when it comes to the Flashlight ship, I can't help but want to bend over backwards, so to avoid doing that, I am just removing Flash Sentry from the equation to begin with.

Extra Info: For the purposes of this fanfic, Diamond Tiara and Silver Spoon are counted as part of the "Cutie Mark Crusader" character tag, even if they are not a part of it in the show.

Published 2021-07-20 23:00:01 UTC
Last updated 2021-10-05 05:52:32 UTC

Takeover Arc: Episode 1 - Finding Help

Not knowing what had become of the Main Six just quite yet, Spike ran to Ponyvile to get help. The young dragon managed to run into Spitfire, Soarin, Apple Bloom, Sweetie Belle, Scootaloo, Diamond Tiara, and Silver Spoon.

“Spike? What’s the big rush?” Sweetie Belle asked.

“It’s Sombra.” Spike said.

“Kind of late to the party there; just got word the main six beat him at the Crystal Empire.” Spitfire said.

“That’s what we thought to but he came back and destroyed the Elements of Harmony and captured Twilight and the others.” Spike said.

“That’s not good.” Scootaloo said.

“We gotta find a place to hide and plan.” Apple Bloom said.

“There’s a cave nearby, we could head there.” Diamond Tiara said.

“Not a bad idea.” Sweetie Belle said.

“We don’t got a lot of time to argue; who knows what Sombra is doing to Princess Twilight and the other elements.” Silver Spoon said.

“She’s right, we better get in and quick!” Soarin said. The group headed into the nearby cave.

Meanwhile, Sombra had finished brainwashing the Main 6. Smiling he released them from his trap and approached Twilight.

“Even brainwashed, your eyes are still beautiful, Twilight Sparkle.” Sombra said.

“Thank you, King Sombra.” Twilight said.

“Now Twilight, don’t you remember that you don’t have to address me by my title?” Sombra asked. “You are going to be my Queen after all.” He added.

“My apologies, I must have forgotten briefly.” Twilight said.

“And don’t worry, your friends are still your friends, they are just generals in my new army. And they don’t have to address either of us by title. After all, your friends are my friends.” Sombra said.

“Hey Sombra, got a question for you.” Rainbow Dash spoke up. Sombra blinked. Funny, he believed their free will to be totally gone.

“Do enlighten me, Rainbow Dash.” Sombra said.

“Once you’ve finished taking over Equestria are you going to create your own flying stunt team akin to the Wonderbolts?” Rainbow Dash asked. Sombra blinked. It honestly hadn’t crossed his mind but he did have to give credit where it was due: The Wonderbolts we’re not only military fliers, but also stunt fliers too. And considering Rainbow Dash is amongst their numbers, and how she handled herself, he had to admit the thought of a similar team to his name was now making a lot of sense.

“Not a bad idea. Hope you wouldn’t mind if a couple of Wonderbolts were brainwashed into joining it.” Sombra said. Perhaps the brainwashing kept their personalities intact.

“Not at all. I was asking because I was hoping I could join up.” Rainbow Dash said.

“Rainbow Dash, I promise you, you’ll be amongst the elites of the new team. Given you’ve already made it into the Wonderbolts Proper, making you part of the initial Shadowbolts Team is a given.” Sombra said.

“Shadowbolts, I remember those.” Twilight said. “When Luna was possessed by the nightmare, she created Shadowbolt illusions to try and trick Rainbow Dash.” Twilight said. That proved it for Sombra: Their main personalities and memories remained untouched.

“Didn’t know she was a fan of the crystal ponies I made into the original Shadowbolt team.” Sombra said.

“Wait you created the Shadowbolts?!” Rainbow Dash exclaimed.

“Guessing someone didn’t know originally.” Sombra said.

“Woo! I can throw a Shadowbolt Recreation Party!” Pinkie Pie said, throwing around confetti that seemingly came from nowhere.

“Trust me Sombra, the sooner you stop questioning Pinkie Pie, the better off your sanity is going to be.” Twilight said. Sombra sweat dropped. He knew that if Twilight; the smartest mare he knew; was saying something like that, it had to be true.

“But more importantly, we better go find Spike.” Fluttershy said.

“The currently infant Dragon? Heh…fool doesn’t even realize I’ve been using my Shadow Magic to track him the entire time.” Sombra said. Twilight hugged Sombra lovingly.

“Then let’s not waste any time; me and my friends will go with you to watch you brainwash Spike and everyone with him.” Twilight said.

“That was the plan anyways.” Sombra said, leaning into the hug. This felt nice. Sure there was some brainwashing done with Twilight to force her to love him, but Sombra had to admit it that this was working to his benefit. Still, something didn’t feel complete yet. He’d figure it out later.

Back with Spike and his group, they managed to enter the cave. They had gone here to try and plan out their next move. Unfortunately, they didn't get very far into planning when both Spitfire and Soarin noticed Sombra with the brainwashed Main Six accompanying him.

"Spike behind you!" Spitfire called out. Spike looked and saw what the Wonderbolts saw.

"Sombra..." Spike said simply. He's brainwashed them completely. Twilight I can understand because he flirted with her back during that time I saved the Crystal Empire, but the others? I don't get it. He thought to himself.

"It's cute how you thought you could escape me, dragon." Sombra said. "But, I expected Twilight to send you off to get help when I destroyed the Tree of Harmony. That's why I've been tracking you with my Dark Magic this whole time." Sombra said.

"WHAT?!" Soarin yelled.

"Ya mean ya planned for this?!" Apple Bloom exclaimed.

"Not cool..." Scootaloo said, trying to be brave but her legs were shaking at the thought of her having to go up against the mare she viewed as the big sister she never got.

"That's just all kinds of wrong..." Diamond Tiara said.

"I never thought I'd say this but Diamond Tiara is right." Sweetie Belle said.

"And I never thought I'd here Sweetie Belle say Diamond Tiara was right about something." Silver Spoon said.

"Oh but wait there's more." Sombra said.

"More? How can there possibly be more?" Spitfire asked.

"Just wait for it..." Rarity said.

"Yer in for a treat." Applejack said. Sombra began to use his brainwashing powers on Spike's Group as soon as Applejack finished speaking.

TO BE CONTINUED...

Author's Note

Gonna fault the show for this: Why weren’t Diamond Tiara and Silver Spoon given more then just cameo appearances after the CMC got their cutie marks? Would’ve been nice to see the two become aids to the CMC after they stopped being bullies. Heck, maybe not even aids, actual CMC members.

Though I have to wonder: Why does the site try to get me to spell correct Soarin's name when there's no reason to do so.

Fun fact: I started listening to music to help keep my mind going with creative juices as I wrote this chapter. Not that anyone ever cares it seems. :raritycry:

Takeover Arc: Episode 2 - The Transformation

Previously, Spike had run into Spitfire and Soarin of the Wonderbolts; as well as the Cutie Mark Crusaders alongside Diamond Tiara and Silver Spoon. After going into a nearby cave with the group to plan, Spike was unaware that Sombra had been using his dark magic to track him the entire time, which lead to the group's location; a nearby cave; to be discovered in a heart beat. Now, Sombra is proceeding to brainwash the lot of them, not wanting to give them any chance of escape. Then again, he did brainwash the Main 6 so Spike's group was at a disadvantage no matter what they tried.

Of course, this sort of thing would be the furthest thing from that group's mind, as Sombra was in the process of brainwashing all of them. It didn't take long for the brainwashing to take full effect. Of course, something was still bothering Sombra.

"Sombra, are you feeling okay?" Twilight asked. "I know something is bothering you, and as your future wife, you shouldn't be afraid to tell me things." She added. Sombra couldn't help but smile.

"I'm not exactly sure. Pegasus child, would you mind stepping forth for me." Sombra said.

"As you wish, King Sombra." Scootaloo said, coming towards Sombra who proceeded to scan her wings with his magic. Rainbow Dash suddenly came forward as well.

"Something the matter, Sombra?" Rainbow Dash asked. Seems that even brainwashed, Rainbow Dash wants to protect Scootaloo.

"You could say that...the pegasus child here is crippled when it comes to using her wings." Sombra said.

"Darn. I was really hoping it was just a phase she could get past and eventually fly. Your telling me she will not ever be able to fly now?" Rainbow Dash asked.

"Wouldn't say that." Sombra said. "Dark magic has advantages Light magic does not." He added. Also, it also gives me an idea. He added. "Twilight, you wouldn't mind if I turned you and every pony here into Dark Alicorns would you?" Sombra asked.

"What about Spike?" Twilight asked.

"I can turn him into a Dark Dragon. I'm sure you'll like the results all the same." Sombra said.

"That sounds cool, but why do you want to do that?" Twilight asked.

"Because, I want to ensure my victory against Celestia and Luna; and even though I'm certain my army could do it, I want all of you to lead it." Sombra said. Twilight smiled.

"That sounds great." Twilight said.

"But what will that do for Scootaloo?" Rainbow Dash asked.

"Well it'll get rid of her crippled state I'll tell you that much. So she would easily be able to fly once she learnt how to." Sombra said. Scootaloo's brainwashed eyes went wide.

"You mean...I can finally be just like Rainbow Dash!?" Scootaloo exclaimed, practically unable to contain her joy.

"I think that's exactly what Sombra means Squirt." Rainbow Dash said, smiling.

"Let's not waste any time then!" Scootaloo said, falling back into formation with the others.

"She sure does look up to you." Sombra said.

"I'm the closest thing she's ever had to a big sister." Rainbow Dash said.

"I see. Then I suppose you want to help her learn to fly properly then?" Sombra asked.

"Do you even need to ask? I so want to." Rainbow Dash said.

"Rainbow Dash, if you would like me and Spitfire to help you, we would like to." Soarin said.

"That would mean a lot." Rainbow Dash said. This was giving Sombra an idea.

"Well since I plan on recreating the Shadowbolts, I could easily make the three of you the first of the elite with Scootaloo also amongst you. Pretty sure with the three of you helping her, she'll be no different then the three of you in terms of flying in no time." Sombra said.

"That would make things 20% Cooler; let's do it!" Rainbow Dash got into formation too.

"Well seems everyone is on board. Might as well join the formation." Twilight said. She gave a kiss to Sombra who kissed back before Twilight joined the others in formation.

Sombra started casting the spell needed to do what he had said he was going to do. The group in front of him was transforming before the Shadow King's eyes.

As this was going on, in Canterlot, Celestia began sweating up a massive storm.

"What...what is this feeling?" Celestia asked.

The transformation of those Sombra was using his spell on was effecting them in different ways. Twilight was already an alicorn unlike the others so she did not change race at all. The only thing that seemed to change was that Twilight went from the purple she's know for being, to a pure black color, with her mane and tail color becoming a dark blue. Silver armor appeared on her, but most important of all was a silver crown put on her head. This was done as an extra thing by Sombra to show that Twilight was his queen.

As for the Pegasi of the group, they all grew horns, but while Fluttershy got cream colored armor, the other four were given uniforms that perfectly matched up with the ones the Shadowbolt Illusions Nightmare Moon created wore. All of the colors of their mane and tail were kept the same.

When it came to Rarity and Sweetie Belle, both were given wings. though just like with the former Pegasi, the former Unicorns also kept their mane and tail colors. Additionally, Rarity had white colored armor with Sweetie Belle being given slightly tinted white armor.

The earth ponies gained both a horn and a pair of wings each; in addition to their mane and tails colors remaining the same, Applejack got to keep her hat, Apple Bloom got to keep her hair bow, Diamond Tiara got to keep her Tiara, and Silver Spoon got to keep her glasses. Additionally, Applejack got orange armor, Apple Bloom got Yellow armor, Diamond Tiara got Pink Armor, and Silver Spoon was given gray armor. While Silver Spoon's armor looked silver, it wasn't. As for Pinkie Pie, outside of getting the usual horn, wings, dark body, and Pink Armor, she didn't really seemed to have changed that much as she was the only earth pony who didn't wear any special accessories.

But of all of them, the most surprising transformation was Spike's; while everyone was still made into the color black outside of their manes and tails, Spike's main body was made black but he kept his green scales. The surprising part of his transformation, was that in addition to a light blue armor that made spike look like a dragon version of Nightmare Moon, Spike was also given a horn.

Wit this, the transformations were complete. Those whose eyes could be seen had dark blue irises but the Shadowbolt members instead had special goggles with yellow lenses over their eyes, but if one peaked, they would see the same dark blue irises like the others. Each one still had their eye color unchanged if one looked close enough.

"Wish there was a mirror here so you could each see yourselves; you all look much better. Especially you, my dear Twilight." Sombra said.

"I'm glad I came out to your liking, Sombra." Twilight said. "Gonna miss the way I colored my mane and tail before though." She added.

"You can always change that back if it's not to you liking. I just thought you could go for a change of pace my dear." Sombra said.

"You always say the sweetiest things." Twilight said, kissing her future husband.

Meanwhile, somewhere in the Crystal Empire, the Crystal Guard found the dead body of Flash Sentry, easily deduced to have been Sombra's handiwork during his take over of that area.

Author's Note

For those wondering about the Celestia bit, I just wanted to put something in here that said "things are going to end well for the good guys" in here.

Also, R.I.P. Flash Sentry.

Takeover Arc: Episode 3 - The Apple and the Tiara

As Sombra created an army in Ponyville with his future queen Twilight, the Shadowbolts were helping Scootaloo out with actually flying.

...Though considering there were three former wonderbolts helping out the formerely crippled Pegasus, that really didn't take too long at all.

"Woo! Go Scoots!" Apple Bloom said.

"Looks like King Sombra really did allow her the ability to fly." Diamond Tiara said. "Kind of wish she didn't need magic to do it; but still, it is nice she's having her dream come true now." She added.

"Ah doubt it was just magic that caused this. Sure her crippled nature is gone now, but that wouldn't have made her able to fly out of nowhere." Apple Bloom said.

"I guess your right. And I can say that I'm happy she's getting her dream come true here." Diamond Tiara said. Apple Bloom was looking around. "If your worried about my mother hearing me say stuff like that, she's gonna have to answer to King Sombra. Getting real fed up with her to be honest." Diamond Tiara added.

"Ah wonder how long it'll take others to find out something you've been hiding from her." Apple Bloom said.

"Probably not long if you drop hints like that. Not that I care, that's just part of your charm." Diamond Tiara said.

"Ah can't help it. It's just so easy to want to tell everyone." Apple Bloom said.

"Well can we wait until after King Sombra takes over Equestria? It'd be safe to announce it to them then." Diamond Tiara said.

"Agreed. Ya always do have good plans Diamond." Apple Bloom said.

"It compliments how smart you are Bloom." Diamond Tiara said. Apple Bloom just smiled.

Meanwhile, in the home of Mr. and Mrs. Rich.

"...Why do I have the sneaking suspecious my daughter is a lesbian?" Spoiled Rich asked to no one in particular.

"Wait a second AB, are you and Diamond Tiara...secretly dating?!" Sweetie Belle exclaimed.

"Guess it didn't take Sweetie Belle long to figure it out." Apple Bloom said.

"How long has this been going on Diamond Tiara?" Silver Spoon asked.

"Ever since the Crusaders got their cutie marks." Diamond Tiara said.

"...Okay now I'm not as upset." Silver Spoon said.

"We've been keeping it on the downlow in case mother found out. Though if she tried anything after doing so, daddy would most likely divorce her because of it." Diamond Tiara said.

"Eh? Why do you think he'd do that?" Sweetie Belle asked.

"Hello, ah'm part of the Apple Family at Sweet Apple Acres and granddaughter of Anny Smith." Apple Bloom said. "Better known as Granny Smith." She added.

"That makes sense." Silver Spoon said.

Scootaloo meanwhile was pratically an ace flier by the time the conversation ended.

"Think King Sombra will agree, your in the Shadowbolts." Spitfire said.

"Way to go Scoots." Rainbow Dash said.

"Thanks Dash." Scootaloo said.

"...Why do I feel like we missed something?" Soarin asked.

"It's good to hear you've progressed so well so quickly." Sombra said.

"I guess I still had the tips Rainbow Dash was giving me back when I really was trying to fly stuck with me." Scootaloo said.

"That's a good thing. Now, what's this about Apple Bloom and Diamond Tiara dating?" Sombra asked.

"Please don't make us split up King Sombra." Apple Bloom said.

"Wasn't going to, but this is the first time I've heard of two mares being in love with the same sex." Sombra said.

"Gee, you obviously didn't get why Lyra and Bon Bon were in bed together then." Twilight said.

"Wait THAT'S why they were in bed together? You mean they were..." Sombra's eyes went wide as his voice trailed off.

"...Ah think you just broke 'im." Apple Bloom said.

"I'm going to need process this later. For now, we march to Canterlot." King Sombra said.

"I'm afraid you will do no such thing." A male voice said. Suddenly Prince Blueblood was there.

"Blueblood." Twilight said, poised to attack.

"You really think you can stop me?" King Sombra said.

"Of course I do. I got back up." Prince Blueblood said and clopped his feet. But nothing happened so he tried again. "...Okay that's not right. Where are those assasins at?" Prince Blueblood asked. Suddenly a sword came out of nowhere and just barely missed the prince before suddenly a young Pegasus stallion in a mech suit showed up to collect the sword.

"I'm afraid your assassins won't be showing up." The Pegasus Stallion said.

"What...who are you?!" Prince Blueblood asked.

"My name is Shade. And I'm afraid this is where you die." The Pegasus Stallion said.

"If you kill me, you'll be an enemy of the crown." Prince Blueblood said.

"I'm afraid that's where your wrong. I'm simply doing my job and preserving history. Your not even supposed to be here, let alone have an army of assassins. So now I have to fix the mess you've created." Shade said. "And don't even try to escape the likes of me. You won't get far." He added.

"That's what you think." Prince Blueblood tried to use his magic to teleport away but then suddenly his head was cleanly slicced right off by Shade at blinding speeds.

"Damn he's fast." Rainbow Dash said.

"Just who are you, really?" Sombra asked.

"Be thankful you surviving is critical to your Equestria's history. Otherwise I would spare you no mercy." Shade said before he mysteriously was teleported away somewhere.

"Where did he just go?" Sombra asked.

"No idea, but we shouldn't waste time here." Twilight said.

Author's Note

DiamondBloom/AppleTiara ship ftw!

Takeover Arc: Episode 4 - Invasion of Canterlot

Prince Blueblood had not checked in yet which was worrying Princess Celestia. Normally she would not be so worried over Blueblood, but something was different about this. Something just felt wrong. As if there was a dark and not all too pleasant reason why Blueblood has not checked in yet.

…She had no idea just how right she was to worry.

"Shade...who the hell was that pegasus?" Twilight asked.

"Beats me. He seemed very edgy though." Sombra said. "And I mean to an extreme degree." He added.

"So, is it about time to conquer Canterlot?" Twilight asked.

"My army is about to march as we speak. All it needs is every one of my generals leading it. Of course, you and I have other business." Sombra said.

"Right. Celestia and Luna." Twilight said. She nearly gagged at the bare mention of those two. Sure friendship was nice and all, but it was time for Equestria to wake up and live in the real world. And the real world didn't have room for weak rulers. Or ones that shouldn't be trusted. Luna was no stranger to turning evil, having been corrupted because of jealousy towards her sister. Whose to say it won't happen again? And as for Celestia, she was no better off, having once banished her own sister to the moon instead of trying to find another way to help her. Because that's what should've been done rather then what was done. Perhaps then the doubt around the two sisters wouldn't be so huge especially when Chrysalis was so easily able to overpower the solar monarch.

"Be honest with me Twilight, do you think you'll be able to kill your former mentor and her sister?" Sombra asked.

"I was thinking, perhaps instead of killing them, we kept them as our slaves. That way, we discourage those that would dare try to rise against us, as they would always see that we are more powerful then the two most ancient alicorns in existence." Twilight said. Sombra laughed in almost pure glee.

"I'm impressed. I have to know though, why do you believe that keeping them as slaves would be a good idea?" Sombra asked.

"Sombra, you trust me right? Then allow me to educate you: If we simply kill the two sisters, then the ponies will have a banner to fly under which would be one of vengeance." Twilight said.

"You think that I'm incapable of quashing resistance?" Sombra asked, questioning this.

"Not at all. But there would always be a resistance. You'd be quite busy continuing to quash resistance after resistance after resistance." Twilight said.

"I guess I can see your point there..." Sombra said.

"But, if we sawed off the horns and removed the wings of the two alicorn sisters, and kept them both around as our slaves, then ponies would see just how powerless they truly are against us. The message would be clear: Join us willingly, or face the consequences." Twilight said. Sombra smiled wickedly.

"Now that is actually a particularly sinister thought." Sombra said.

"It would also be contining revenge against them too for you. Why bother ending it by taking their lives? They trapped you for a thousand years in the frozen north. So why not make them feel inferior to you for at least a thousand years before you decide to kill them?" Twilight asked. Sombra laughed.

"Now I'm really glad I made you my queen. Giving them a punishment of serving us for a thousand years plus to make them understand just how powerless they are towards us...now that's something I can get behind." Sombra said.

Celestia and Luna were both nervous. They could both feel that something wasn't right. They had sent out the royal guard to check for any intruders. This was three hours ago. Not a single royal guard has returned. As such, the two sisters were ready to fight back but were soon quickly overwhelmed when they were suddenly ganged up on by not one, but five dark alicorns. Luna was quick to be defeated, but Celestia tried to hold on. But then, just as her vision began to fade, she suddenly saw what looked to be Twilight. But deep down, Celestia knew...this was no longer the same mare that she had mentored. As Celestia's vision faded, she heard an all too familiar laugh.

"I'm going to enjoy breaking them, making them forget who they were." Sombra said.

"I'd love to help you, dear." Twilight said, smiling.

"I'd like that, my dear Twilight." Sombra said, smiling back. The pair soon kissed.

Canterlot fell that day. But the takeover was not yet complete.

Author's Note

Believe it or not, there is still more to this story ark incoming. And I cut this off here just because I wanted to do a little something else. You'll see what I mean shortly. Also, while I am posting this on a Monday, it is like 3:20 AM at the time of making this and I want to write something else today too.

Takeover Arc: Episode 5 - The Crystal Empire Takeover

"Now that Canterlot is fully under my control, the next step is the Crystal Empire." Sombra said. "And I am a stallion of my word; no harm will come to your brother and sister-in-law." He added.

"They do have a child, but I'm hoping you'll spare her too." Twilight said.

"They must have hidden said child from me when I was there..." Sombra admitted.

"Actually my niece ended up staying at my castle in Ponyville." Twilight admitted.

"Clever...but I suppose I'll spare her life too. After all, the mind of a child can be more easily corrupted." Sombra said, grinning evilly.

"Things don't feel right..." Shining Armor said. "First we discover that Flash Sentry committed Suicide, and now there's been no word from Equestria." He added.

"Shining please; you worry too much for your sister sometimes. Yet, I can't help but share your worry this time." Cadence said. "Something feels wrong. I just know it does." She added. Flurry Heart shifted uncomfortably in Cadence's hooves.

"Even Flurry Heart seems to feel that something is wrong." Shining Armor said. Suddenly, a wounded crystal soldier began to limp his way in.

"What happened?" Cadence asked.

"It was...Sombra...he...he..." The soldier soon passed out from his injuries.

"But how did he survive getting blasted by the elements of harmony? That makes no sense!" Shining Armor said.

"Unless...he managed to get away from the blast at the last second..." Cadence said, before gulping.

"That is NOT good..." Shining Armor said. "Seems I was right to worry after all." He added.

"For once, I'm glad you were worrying." Cadence said.

Sombra's forces were relentless; and Shining Armor had no idea just how his forces got so strong in the first place.

"There's not much time. Take Flurry Heart and get out of here!" Shining Armor said to his wife.

"I understand. I love you." Cadence said and grabbed her daughter.

"I love you too." Shining Armor said. Cadence began flying off. her back was turned when the doors to the room were opened and a certain somepony was in Shining Armor's view. "! N-no way...it can't be..." Shining Armor said.

...

The only thing Cadence heard after that was an evil feminine laugh. Despite this, Cadence continued to fly away before she was suddenly tackled to the ground by four different dark alicorns. Cadence gasped once she recognized one of them.

"That...explains a lot but still..." Cadence said. Sombra soon approached her.

"An effective strategy your husband had, it's just a pity that I was ready for it. Thanks in part to my own wife." Sombra said, grinning evilly.

"You...you corrupted Auntie Luna...didn't you?" Cadence asked.

"Bah. Why would I dare waste my time with one whose not even related to Radiant Dawn?" Sombra said. "Imagine my surprise when I found out a little something about your Twilight Sparkle. Being dead has it's advantages for several things after all." He added.

"What...do you mean?" Cadence said.

"Here's a fun fact: Twilight Sparkle is the great great great great great great great great great great grandaughter of Radiant Hope. Bet you didn't know that, did you?" Sombra asked.

"What's that got to do with..." Cadence said before Twilight suddenly popped in with a teleport spell. "...No..." Cadence said.

"Hello sister of mine." Twilight said, smirking evilly.

"You corrupted Twilight...oh...oh celestia..." Cadence said.

"Funny thing is, I heard she was going to take over for Princess Celestia. But where would that end up? Now that Twilight is an Alicorn, she's immortal. And it wouldn't have taken long once all her friends as well as Spike were dead for her to start to hold an anger in her heart. And while I may be someone who you call evil; I am not heartless. Now Twilight will be with her friends forever more." Sombra said, grinning evilly.

"How...could you...Twilight would never..." Cadence tried to argue.

"The future is never set in stone." Twilight said. "It always fluctuates. Even if that requires that evil win sometimes." Twilight said.

Cadence couldn't help but shed tears as Sombra began to brainwash her.

Far away, outside of Equestria, a certain Draconiquis was moping.

"What have I done?" Discord asked no one in particular.

Author's Note

I know this chapter is shorter then the others so far, but I couldn't find enough context with what I wanted to do next that wouldn't make things seem like I was rushing things. It's worth noting that at this time, none of the villains that Discord brought together; this being Sombra, Tirek, Chrysalis, and Cozy Glow; know that Grogar was Discord in disguise. So please, keep that in mind for later.

Takeover Arc: Episode 6 - Loose Ends Part 1

"So, Cozy Glow, Lord Tirek, and Queen Chrysalis were also freed? And you want to be rid of them all?" Twilight asked King Sombra.

"If there are no objections to that." King Sombra said.

"King Sombra, a moment." Apple Bloom spoke up.

"Go ahead..." King Sombra said.

"Cozy Glow may have tricked us, but we still kind her to be one of us." Sweetie Belle said.

"We were wondering perhaps...sparing her? Let her be with us? We'll keep an eye on her, we promise." Scootaloo said.

"What brought this on Scoots?" Rainbow Dash asked.

"Like you have mentioned, I'm not exactly sure if she can be trusted; even if brainwashed." Twilight admitted.

"We'll convince her! I know we will! Besides...if she's good..." Scootaloo shook her head. "A-anyways, you can just let us look after her until she proves one way or the other." She added.

"Hrr...I'm just not sure." King Sombra said.

"You do realize that if me and King Sombra agree on this, that puts you in charge of her 100%. Got that?" Twilight said.

"Yes Queen Twilight." Apple Bloom said.

"No take backs either. If you can't handle her, then she'll be killed. Do I make myself clear?" King Sombra asked.

"We'll be having Diamond Tiara and Silver Spoon help; it can't be that hard for five dark alicorns to keep a lid on the one can it?" Sweetie Belle asked.

"It is Cozy Glow, but you raise a good point." Twilight said.

"Perhaps, but I won't be making her a dark alicorn. Not unless she willingly submits to my will." King Sombra said. "And only then. Until then, you better hope the five of you can handle her." He added.

"You got it!" The CMC all said at once.

"Now as for this Grogar character, any idea how to lure him out? The other three are pretty easy." Twilight said.

"We'll worry about that later." Sombra said.

"Hmm? A letter? For me?" Chrysalis said. "...Huh? A letter from my hive? Welcoming me back? Wait...why?" She asked.

"Well talk about miss lucky pants. You should go see what's up with that." Cozy Glow said.

"How rude child!" Chrysalis said. "But your right none the less, this requires my immediate attention. If Grogar comes back, tell him that something majorily important has come up." She added before leaving. She was heading for the swamp when suddenly something jumped her. When Chrysalis looked at her attacker, she gasped. "...It...can't be..." She said.

"Hello Chrysalis." Shining Armor said, grinning. He was now a Dark Alicorn just like his sister. "I've been meaning to do this to you ever since you kidnapped me, my wife, and my child." He said. All that came out of Chrysalis's mouth then and there were screams of pure pain.

"My brother wishes to see me? Now? After all these years?" Tirek said as he got a letter from his brother.

"A-at least your family still cares about you somehow. Even after you've gone all evil. Plus, well...at least your brother is willing to see you. Look, I know you and he had problems in the past, but...maybe just this once...instead of seeing him as a traitor, you should see him as a brother. Family is...something you shouldn't take for granted if you have it." Cozy Glow said.

"What do you know about family?" Tirek asked.

"Family is...something you should not get rid of, I'll just say that much." Cozy Glow said. "I just wish mine would take me back..." She added.

"What was that?" Tirek asked.

"Nothing. Just go. Go run to your brother. And even if it's not like you, give him a hug. In fact make that two; tell him the other one is from me." Cozy Glow said. "And if you can...come find me. I'll probably jolt after a while more here. Go see what I can do now that I'm free." She added.

"Your probably going to want to avoid breaking laws." Tirek said. "Or being spotted." He added.

"I'll come up with some kind of plan...just go already. Don't worry about me." Cozy Glow said.

"Meh..." Tirek said and left. But if he had stuck around, he could've heard Cozy Glow start crying.

"...It's not fair...It's not fair...it's not fair..." Cozy Glow said. "I'm all alone again. No family...no friends...I'm all alone all over again..." She said before she began to sob relentlessly.

There was someone watching her break down.

"...Queen Twilight's gonna flip when she hears about this..." A female voice said; their voice barely above a whisper.

Meanwhile, Tirek would never find his brother, instead, Queen Twilight personally executed him herself.

"It's just not fair..." Cozy Glow said as she began packing things to go off. "But at least they have families to go to now. Unlike me. After I was born a Pegasus over a unicorn, my parents disowned me! The first moment that they could, they dropped me off at that adoption place and never wanted to see me for the rest of their lives! I got adopted by two pegesi eventully, and when I was six years old, they told me that I was adopted. I managed to find my real parents and they...they told me everything! So I wanted nothing to do with them or my adopted parents so I fled. I fled as far as I could." Cozy Glow said. "And now...now I have nothing again..." Cozy Glow said as she began to break down.

"Oh...Oh Cozy Glow..." The spying female said; her voice still barely a whisper. "Queen Twilight needs to hear this..." She added.

"WHAT?!" Twilight's voice was loud, and Sombra felt like his ears were going to burst from his wife using the patented royal Canterlot voice.

"MY EARS!" Somba shouted as he was right next to his wife.

"She didn't even know I was there the whole time but...I swear that's what she said." Scootaloo said.

"Oh my..." Twilight said. "That changes things..." She added.

"Let me guess, you were going to use the same ruse on her as the other two?" Sombra asked.

"Yes but...I can't now. Not like this." Twilight said.

"I'll write her a personal letter. Maybe that could work instead." Scootaloo said.

"That could work, yes." Twilight said. Scootaloo nodded and left.

"...Gee...wish we had known THAT sooner." Rainbow Dash said.

"Tell me about it." Twilight said.

Takeover Arc: Episode 7 - Loose Ends Part 2

As Cozy Glow continued packing her things, she didn't notice a letter being left for her by someone who had heard her confess some things. Still, Cozy Glow managed to find the letter anyways.

"It's from Scootaloo? I wonder what she's writing about." Cozy Glow asked. "Something doesn't feel right now that I think about it though. How did anyone know me, Tirek, and Chrysalis were even here. Though maybe Grogar managed to intercept these letters. I mean, I suppose if the dude can make Tirek get muscles and revive that King Sombra guy, he can do anything he wants." Cozy Glow said and opened up the letter.

Hey Cozy Glow, listen...if you at least care somewhat...me and the crusaders were talking and we got Princess Twilight to consider releasing you from tartarus under her supervision as me and the crusaders would really like to be your friends for real. That is, if you promise not to try and conquer equestria anymore.

Princess Twilight somehow managed to find your parents and they wanted nothing to do with you and it really made her upset at them. She even gave them an hour long lecture if Rainbow Dash is to be believed. I've also somehow managed to be able to fly now. So I really want to show that off to you. Another reason why I hope you'll agree to this whole thing.

Besides, do you REALLY want to be an empress? From what Princess Twilight said about Princess Celesta, she's constantly swamped with paperwork, and I don't think you want that sort of thing for yourself. And even Princess Twilight herself has her own paperwork to work through and it's insane how much there is. So I think your better off not going for being a ruler of any kind.

I Hope you'll consider everything and hope to see you soon. -Scootaloo

"Bleh...I think I would hate paperwork. So maybe just chilling and being with the CMC would be better for me anyways. At least then I'll have SOME friends." Cozy Glow said. "Still, something doesn't feel right about this whole thing but meh. I think she's serious." She added and started flying off.

However, just as she left, Grogar came back. And he was not looking happy. "...Dammit...I got here too late." He said. It was not really Grogar but rather Discord disguised as the ram in question. "...There's no hope left..." 'Grogar' said.

Cozy Glow proceeded to head for Ponyville, not really aware of what would be awaiting her. Meanwhile...

"Are you sure this is the way you want to play things?" Twilight asked Scootaloo.

"Trust me, this is the way I think we have the best chance." Scootaloo said.

"Well I trust you." Twilight said.

Right now, Scootaloo and the Cutie Mark Crusaders looked as they did before Sombra turned them into Dark Alicorns, but also with fake bruises and a damaged ribbon on Apple Bloom's head. They made sure it was one of Apple Bloom's own though.

"Are you really sure yer fine with losing that ribbon after this?" Applejack asked her sister.

"I have a whole drawer full of the things big sis; losing one for this is a worthwhile exchange." Apple Bloom said. Rainbow Dash showed up.

"She was just spotted coming this way. Places." Rainbow Dash said.

"Now or never." Scootaloo said and laid down, feigning being heavily injured. The other two cutie mark crusaders joined her where as everyone else hid.

"Gonna have to admit, if this works, it's the most clever plan I've ever seen." Diamond Tiara said.

"Too true." Silver Spoon said.

"Now where is Discord at? Queen Twilight is going to want his powers all to the royal couple." Fluttershy said, as she was flying places with the rest of the Shadowbolts keeping an eye on her.

"You seriously want that Draconiques alive?" Soarin asked. "After everything evil he's done?" He asked.

"Are you questioning her, Soarin?" Spitfire asked.

"N-no captain." Soarin said.

"Good. Because you should know better. Do you want her to give you The Stare?" Spitfire asked. Soarin gulped when he realized what his captain was referring to.

"Thought you didn't believe in that though?" Soarin said.

"Didn't use to believe in it, until I upset Fluttershy something fierce with her animals which she has brainwashed into serving King Sombra. I questioned her about them and...well...let's just say when we get back to Ponyville, I owe Dash an apology for not believing her when she said to not mess with Fluttershy and her animals." Spitfire said.

"Wait...you mean you...?" Soarin asked.

"Yep. I got The Stare from her while you were helping Dash get the CMC's plan for Cozy Glow ready." Spitfire said. "It's real as anything else out there, that's for sure." She added. Soarin gulped.

"Hey wait, what's this up ahead?" Fluttershy asked.

"That's Death Vally; not a lot of ponies come out this way." Spitfire asked.

"Hey wait a second..." Fluttershy flew up a bit. "I see it! I see the cave his majesty mentioned!" She added.

"Wow." Spitfire said.

Though when they all got in there, they saw a sight that made them all scream. Fluttershy the loudest of all.

Meanwhile, Sombra's ears started ringing out of nowhere and he had to hold his hooves to his ears.

"What is it Sombra?" Twilight asked.

"I dunno...I think I just felt like someone screamed so load, it was enough to pierce my eardrums." Sombra said.

Cozy Glow was flying and came across the Cutie Mark Crusaders doing their act. Cozy Glow gasped and flew down to them.

"Scootaloo? What the heck happened to you guys?" Cozy Glow asked.

"It was...Sombra...he...came out of nowhere...he's after Twilight..." Scootaloo said, voice strained.

Fucking Cheater...he's already failed. Cozy Glow thought to herself. Now was not the time for that though. "Just tell me where he's going, I'll try and slow him down..." Cozy Glow said. Suddenly she was blasted.

"I think not..." Sombra said. He then proceeded to brainwash Cozy Glow and turn her into a Dark Alicorn.

Later, it would be told via Fluttershy that Discord was found to have committed suicide. Everything seemed to have turned out in Sombra's victory.

Takeover Arc: Prologue - Tree Destruction

The Main 6 managed to defeat Sombra using the Elements of Harmony and have arrived to return the Elements of Harmony to the Tree of Harmony

Mistakenly thinking all was well in the world, and that they could focus on who it was that brought Sombra back to life; let alone how they managed to do so; the group plus spike turned to leave...

However, before everyone could get very far, Sombra appeared again and this time destroyed the Tree of Harmony, laughing at the Main Six and telling them how they lead him right to the source of their power.

In the original timeline, this would be where Sombra would trap the main six and Spike so he could brainwash Ponyville into marching onto Canterlot.

However, this is not the original timeline, and as such, things are going to play out much differently here...

"No! Not the elements!" Twilight said. "Spike, get out of here, you've got to go get help!" Twilight said.

"Okay Twilight, I'm on it!" Spike said and left to go get help avoiding Sombra's trap.

"How interesting that you'd send him off, knowing he's defeated me before." Sombra said addressing Twilight. "Sadly, he won't be able to this time, not with what I have planned." Sombra added.

“Your not leaving, meaning you want us for some reason.” Twilight said.

“Just as smart as before. Seems becoming an Alicorn did nothing to that mind of yours.” Sombra said.

“Trying to butter me up again, Sombra? It didn’t work the last time you flirted with me.” Twilight said.

“He did what now?” Applejack asked.

“I…didn’t want to talk about him flirting with me. I mean really, who just does that to a stranger.” Twilight said.

“You think I spent my time being sealed away let alone dead just twiddling my thumbs? Thought the brainwashing I did on the crystal empire proved that wrong.” Sombra said.

“What’s that supposed to mean?” Rainbow Dash said.

“Radiant Hope.” Sombra said. “That’s the name of Twilight’s ancestor. Found that out while sealed away. And it shows.” He added.

“What’s that got to do with you?” Twilight asked.

“Radiant Hope was the only pony who wanted anything to do with me.” Sombra said. “However, I do have to say, you are quite the beauty all the same.” He added.

“Stop. Your flirting didn’t work to manipulate me the last time, and it certainly won’t work this time.” Twilight said. Sombra laughed. “What’s so funny?” Twilight asked.

“You still haven’t figured it out? And I thought the hints were obvious.” Sombra said. Twilight’s eyes went wide.

“It doesn’t matter that your words won’t work on me, does it?” Twilight asked.

“Good, your catching on.” Sombra said.

“Twilight, what do mean it doesn’t matter?” Pinkie Pie asked.

“Because he doesn’t need to worry about his words falling flat on me.” Twilight said.

“But any stallion flirting with you is kind of a big deal.” Rarity said. Everyone just stared at her. “…Well maybe not him.” She added.

“It doesn’t matter, because he plans on using other means of convincing. Not just on me, but all six of us.” Twilight said.

“Um…you don’t mean…” Fluttershy caught on.

“I do.” Twilight said. “I wish I was wrong but why else not chase after Spike? Why stay here and begin with flirting with me? Why drop all that talk on us at all?” She asked.

“Just like I thought: You figured it out.” Sombra said

“Your going to brainwash us. It doesn’t matter that I’m not falling for your flirting; you just going to brainwash us. After all, you want to use us as leaders of your army.” Twilight said.

“Well that applies to your friends. You Twilight, will have a better place in my empire.” Sombra said. Twilight gulped.

“You…your going to…to make me your Queen…” Twilight said.

“You should feel honored. But do not fret, once you are brainwashed, I will not treat you as a slave, but as an Equal.” Sombra said.

“Even now you still attempt to flirt with me…” Twilight said.

“Better get used to it, my sweet sweet Twilight. You won’t be able to resist it for long.” Sombra said as he got to the brainwashing.

“Just…promise me…one thing…” Twilight said, resisting as best she could. “You’ll…let me…at least…still have…my brother…and sister-in-law…” Twilight added.

“Twilight, outside of Celestia, Luna, and a few others, everyone will live.” Sombra said.

“That’s…fair…enough…” Twilight said before she fell under the brainwashing alongside her friends.

Besides, I may be a Tyrant, but I’m no killer to those I can use. Sombra thought to himself.

Story Prologue - Evil Wins Sometimes

Second Person, P.O.V.

The Library of Official History. You've Finally found this place. Rumors and myths have lead you to try and find it to see if it really exists. And now as you stand before the steps leading to the double doored entrance, you can hardly believe how real it looks; let alone how it feels as you enter the place.

"Welcome traveler." A male voice greets you as an Anubis-like creature waiting for you at the entrance. "You have travelled far in search of this place, and I welcome you into it's halls. You may call me The Jackle; overseer and archivist of the history of all worlds alongside their alternate branches." He finishes speaking.

You tell the Jackle that your name is [your name] and you have come here to see if the place really does exist. The Jackle smiles.

"Believe me, it might look unbelievable to your eyes, but rest assured, everything you see is real." The Jackle said.

You tell the Jackle to prove to you that this place is as real as he says it is.

"Perhaps this will convince you." The Jackle said, handing you a book. It's tittle was My Little Pony: Friendship is Magic.

You can't help but gasp at this. This book as the same title as your favorite show, and you tell The Jackle as much to which he simply laughs.

"Did you really think the universe you live in is the only one out there? Each of these books contains stories of various other universes, and the alternate histories of their alternate realities, ones where things happened that changed but still lead to endings. Some of these stories are still being written, even as we speak, while some others simply have stopped having updates without a proper ending." The Jackle said.

You ask The Jackle to clarify what he menas by alternate realities.

"Are you familiar with the Many Worlds interpretations of the scenario regarding Shrognigner's Cat?" The Jackle asked. You nod your head. "That is essentially what I mean: There are some instances where certain things happen that cause a new version of a world to be born, split from the prime timeline of events. Sometimes, those stories have good ends, but other times, they have bad ends. But it is a necessity for some timelines to end up with bad endings where evil wins, as it creates a balance." The Jackle explained.

You ask the Jackle if he would show you one of the versions of My Little Pony: Friendship is Magic that has a bad end.

"I was waiting for you to ask that question. I believe I have just the story in mind for you." The Jackle said and levitated a book to your hands.

The title of it was Empire of Darkness. Wanting to know where this timeline split off from the original one, you opened the book up to the first page...

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EMPIRE OF DARKNESS