Forget about imprisoning the villains, making them live together was bad enough.
Yes, Princess Celestia really thought up the most terrible and torturous punishments. The last thing that Discord, Queen Chrysalis and King Sombra heard her tell them was 'I'm sure you'll get on great'. Let me tell you, just because they are/were evil, does not mean that they get on well. At all.
So, the three of them lived in a massive house in Faust-knows-where and tried to talk to each other as little as possible. Well, only Queen Chrysalis and King Sombra tried to do that, Discord's goal in life was to annoy them as much as possible.
“DISCORD!!!!!!” Queen Chrysalis screeched, storming out of the bathroom, “DID YOU HAVE TO REPLACE ALL THE WATER WITH GAK????” she found the draconequus and unicorn king lounging around in the living room.
Discord looked up from his book innocently and Chrysalis knew something was up, because Discord never read, not even if his life depended on it. “Whatever gave you that idea?” he asked and King Sombra snickered.
Queen Chrysalis glared at the two of them and wished not for the first time that there was another female in the house. “Maybe because you seem to love hating me?” she spat.
“Oh, but you are so fun to hate.” Discord mused, transforming his book into a lizard and throwing it across the room, “And in case you were wondering, I did not replace the water with gak. You can link everything gak-related to Sombra.”
“I should have known.” Chrysalis muttered, glaring at the grey unicorn who was muttering about stairs. “I stopped wondering about his mental health ages ago.”
“I not mental.” Sombra growled, “Like stairs. That all.
“You're not mental like stairs or you're not mental, you like stairs?” Discord asked with a smirk.
“Latter.” Sombra growled.
Chrysalis laughed, “You don't like stairs.” she said, “Admit it, I've seen the Crystal Palace, you freaking love stairs!”
“Shut up, Cheese-Hooves.” Sombra spat.
“Hey!” Chrysalis cried, suddenly realising how much her hooves resembled cheese and trying to hide them behind one another. Which, of course, was impossible.
Before anything else could happen, there was a flash of midnight blue light, the room filled with smoke and a dramatic female voice said, “Why hello, my little subjects. It has been so long.”
“What in Tartarus?” Chrysalis muttered, “Who are you?”
“Don't you know who I am? Mwahaha!” the voice cackled evilly.
“Can't see. Stupid smoke.” Sombra growled and there was the sound of someone tripping over something and swearing loudly. "Bucking Tartarus!"
“Hahaha! You are no match for the mighty-”
“Oh for goodness sake!” Discord sighed, “We know it's you, Nightmare Moon.” a second later, the smoke cleared and Chrysalis saw the armoured black Alicorn standing in the centre of the living room.
“My dramatic entrance!” Nightmare Moon gasped in shock, looking absolutely horrified, “How can you just get rid of my drama like that?”
“Hate your stupid drama.” Sombra growled, crawling out from behind the couch.
Nightmare Moon frowned down at him, “Did you just trip over the couch?” she asked curiously, "How is that even possible?"
“We live with Discord. Anything is possible.” Chrysalis told her, “What are you doing here?”
Nightmare Moon shrugged, “Oh, Luna thought it would be a good idea to send her evil side over here to annoy- I mean, to be redeemed. Naturally, I didn't like that idea, but I really can't argue because how can you argue with yourself?” she sniffed, “But I accept my sentence. How hard can living with other villains be?”
“Since you're living with the moron and the senile king, it's impossible.” Chrysalis told her.
Discord sighed, “And I suppose I'm the moron, aren't I?” he questioned.
“Who's senile king?” Sombra asked curiously.
“Er, no one.” Chrysalis muttered quickly, “My imaginary friend.”
“So, what do you guys do to pass the time?” Nightmare Moon asked them, “Do you fight? Do you make peace?” her dark eyes sparkled, “Do you make cake?”
“Actually, we just try to avoid each other.” Discord told her, “Well, they try to avoid me while I try to create as much havoc as possible, but then, that is what I was made for, is it not?”
“You made by accident.” Sombra stated.
Discord's eyes widened three times the size they were before and exploded, causing everyone to jump. “Oh, how can you say that?” he exclaimed dramatically, freaking the heck out of everyone in the room.
“This guy needs hobby.” Nightmare Moon said to Chrysalis, who murmured in agreement. “I've got an idea! Why don't we make cake?” everyone looked at her blankly. “What?”
“What's cake?” Asked Sombra.
Nightmare Moon's eyes practically popped out of her head, “You don't know what cake is?” she screeched.
“I don't know, either.” Chrysalis admitted, “But you can't really blame me, I live off love and detest the taste of regular pony food.”
Nightmare Moon began wailing and Discord threw his arm around her shoulders, “Then we must make cake right away!” he exclaimed, “Who knows how to make it?” when empty silence and blank stares followed his words, he smirked, “Then this will be fun.”
Chrysalis slipped away from him, “Actually, I'll be fine just sitting in my room.” she said.
“Sombra too.” King Sombra muttered, turning into dramatic black vapour with eyes and floating out of the room.
“Hold it!” Discord exclaimed, grabbing onto Vapour-Sombra and turning him back into a unicorn, “This is going to be fu-u-un! Why run away, we'll be having a great time!” he pulled the other three villains into a massive group hug.
“I hate you.” Nightmare Moon said as best she could with her face squished into Discord's armpit. Sombra and Chrysalis heartily agreed.
“Ok, we need to set some rules, since this 'kitchen' can be a very dangerous place.” Chrysalis stated, eyeing a spatula that was sitting on the counter distrustfully. “Since none of us has ever made as much as a sandwich for ourselves – some I don't even think have done that,” she glanced at Sombra, “I know I haven't made any disgusting pony food, so you're not alone.”
“Get to the point.” Discord sighed, “This is boooooring!”
Nightmare Moon scowled at him, “Sometimes, following rules stops you from getting killed.” she told him.
Discord smirked, “I've taken my eyeballs out of my head and didn't bleed to death.” he told the black Alicorn, “Beat that, Nightmare Loony!”
“Hey, the only loony here is you!” Nightmare Moon spat, “Compared to you, Sombra is sane.”
“Toldya Sombra's sane.” King Sombra said smugly, “Very, very sane.”
“Yes, yes.” Chrysalis agreed, “You are extremely sane. Anyway, back to the rules, most of these apply to Discords, so I recommend listening instead of turning the sugar into mice.”
Discord looked up from his work, “Come on!” he exclaimed, “Have you never heard of Sugar Mice before? They're delicious!” he shoved a pawful of the mice into his mouth and everyone backed away slowly.
“Anyway...” Nightmare Moon continued, trying not to wonder if the mice Discord was eating were really made from sugar, “Err, here are the rules!” using her magic, she carved the ten rules onto the kitchen counter.
1. Flour is not cocaine, no matter how much Discord insists it is.
2. If Discord tries to turn the flour into cocaine, beat him over the the head with a rolling pin and send him to his room without any cake.
3. Her highness, Queen Chrysalis is not allowed to try and kill anyone with any type of cooking implement (that includes drowning someone in dish water).
4. Discord's head does not belong in the oven, no matter how much anyone wishes it to.
5. Baking is not a game of survival where only one gets out alive.
6. Ponies/Changelings do not eat crystals or whatever you find under the sink. I don't know about King Sombra or Discord, but everyone knows it is unhealthy to place such substances in food.
7. Rat poison will not be used to substitute icing sugar.
8. Nopony is permitted to spit in the cake mix.
9. Frying pans will only be used for cooking and as a form of self-defence. Anypony found engaging in any other activities with a frying pan will be locked in the pantry with nothing but pickled onions to keep them company.
10. “Because I'm paired with Princess Celestia.” Is not an appropriate excuse for breaking any of these rules.
“What do you think?” Nightmare Moon asked proudly, pulling King Sombra's head out of a bag of flour.
“Rule number 4 would be hard to accomplish.” Chrysalis told her, glaring at Discord who grinned, took his head off, placed it into the oven and closed the door, “How the heck does he do that? It's creepy!”
“Why, of course it is!” Discord's head laughed, his voice slightly muffled from the oven's door, “I bet you can't do that!”
“Yeah!” Sombra growled, immediately trying to remove his own head with little success.
Nightmare Moon facehoofed herself, “Alright, let's start making this cake now, because I have a feeling that if we don't, somepony's going to kill someone before we even begin.”
Needless to say, things went off to a bad start.
First, Nightmare Moon found several large bite marks in the only block of butter and gave a stern lecture about hygiene to everypony while Sombra stared innocently into space. Then came the gruelling task of cutting off all the parts that had touched the culprit's mouth, leaving a very small lump of butter to use for the cake.
Chrysalis glared distrustfully at Discord, who stared back at her. “What?” he asked.
“What did you do to the flour?” she asked suspiciously, “You didn't turn it into cocaine, did you? Because you were given explicit instructions not to do that.”
Discords eyes rolled (literally. They went all the way across the room), “Of course I didn't do that! Why would I even dream of breaking such an important rule?”
“Because you like?” Sombra guessed.
Discord sighed heavily, “King Coo-Coo has caught me.” he mumbled sadly, “Oh, how could anyone guess my motives for such lovely chaos?” he dramatically swung his arm and knocked over the large bag of flour, causing it to fall to the floor, spill open and cover the kitchen and everypony in it in a storm of white powder.
“Please don't tell me this is cocaine.” Nightmare Moon muttered, trying hard not to breathe any in.
“It no cocaine.” Sombra confirmed, sneezing in her face and sending up a large cloud of flour that turned into brightly coloured butterflies that appeared incapable of moving away from the mare of darkness's face.
“Now that was me.” said Discord.
“Thank you, I totally did not realise that.” Nightmare Moon growled, using her magic to dispose of the flour on her. “You're even more annoying than I remember you being.”
Discord laughed, “Why thank you!”
After bringing out another bag of flour, keeping Discord safely away from it and carefully measuring out exactly two cups of it, the team of baddies began to once again, pick up some confidence.
“We can do this!” Chrysalis exclaimed as she shoved the bag back into the pantry. Even Discord helped by not pushing her in and locking the door.
It was a chocolate cake, so naturally the whole kitchen got covered in a brown powder shortly after the flour incident when Chrysalis had trouble opening the box of coca powder. Sombra had tried to help by freezing the powder into crystals, but that just complicated things further as nopony had any idea how to get rid of them without smashing the entire kitchen up.
Needless to say, that's exactly what happened.
“Right.” Nightmare Moon muttered, putting the mixing bowl with the butter, flour and coca powder that she'd managed to shield from the other villains onto what was left of the counter. “Sugar. We need sugar.” she turned to Chrysalis, a slightly mad gleam in her eye. “You must get me the sugar now, I'll open it. I know how to be careful.”
Cautiously, Chrysalis spoke of another idea, “Maybe we could just give up and you three could order a pizza?” she had no idea if any pizza store in Equestria would deliver to them, but she as sure as Tartarus was ready to try.
Nightmare Moon's dark eyes grew wide enough to make Discord impressed, “Never!” she snarled, “The great Nightmare Moon never admits defeat!” she cackled madly, diving across the kitchen to collect the box of sugar and Chrysalis wondered which one of them made her snap.
“And you call Sombra crazy.” Sombra muttered under his breath.
Discord grinned, “Another insane buddy!” he cheered, “All we have to do now is convert Chrysalis!” he observed her with his red and yellow eyes, “I must say, she's holding onto her sanity rather well...”
“I swear, you'll never make me snap.” said Chrysalis stubbornly, folding her forelegs across her chest.
Discord laughed, “Oh, just wait.” he said, “Luna told me the same thing the first time we met.”
The three of them looked over at Nightmare, who was giggling insanely while pouring the contents of the sugar box into her mouth. “Should we help her?” Chrysalis questioned.
“Nah, she's fine.” Discord told her matter-of-factly. “I'm sure that in a few days, she'll be converted into somepony just as insane as me!”
Chrysalis sighed, “I think I'm the only sane pony left in this house.” she muttered to herself.
"And me." Sombra put in helpfully.
"Huh? Oh yeah, and you." she added, but more to keep on the insane tyrant's good side than to actually tell the truth.
Chrysalis lay on a couch in the living room, happily reading the latest Daring Do book when she heard a heavy panting sound. Guessing that it was either Discord or Sombra being completely normal, she ignored it and turned the page.
Daring stared up at the giant golden artefact. Never before had she seen such detail and skill used to craft such a-
"Chryyyysaliiiis..."
Chrysalis closed her eyes, "Sombra," she said, "please shut up and find something better to do. Go... Go raid Discord's underwear drawer or something."
"Chryyyysaliiiis..."
"I know Discord doesn't wear any underwear, but that doesn't stop him from having an underwear drawer. Just please leave me alone."
The panting stopped and Chrysalis went back to her book.
Ducking and weaving through the maze of traps, Daring steadily made her way to the base of the statue. After rolling out of the way of a deadly poisoned arrow, she came to a stop at the feet of the giant Alicorn. She knew she didn't have much time left, so she had to work quickly to-
A heavy, dark thing landed on the Changeling queen's stomach, "CHRYSALIS!!!!!!!"
"Oof- Holy buck..." she groaned, dropping her book and rolling off the couch, clutching her abdomen, gasping for air, "Holy mother of-"
"I succeeded." Nightmare Moon said, a smirk playing upon her features. Her body was bruised and her horseshoes chipped, her long mane was matted and scorched, sweat ran down her pelt and yet, she levitated a completed chocolate cake in front of her with her magic. "You all shunned me, you all said that I couldn't do it and I have proved you wrong by crafting this masterpiece with my own hooves!" she laughed haughtily, "I would like to see you create something so wonderful!"
While Nightmare Moon was speaking, Chrysalis had managed to teach herself to breathe again and sat back on her haunches, staring at the cake with utmost admiration in her eyes. "That's... Actually pretty impressive." she said at last, "I thought that Discord had booby-trapped every inch of that Faust-damned place."
Nightmare Moon nodded, "Oh yes," she said, "he had..."
"Huh? Oh yeah, and you."
Nightmare Moon gritted her teeth and tried to block out the silly little argument the pathetic mortals were having behind her. She was Nightmare Moon and she was going to prove that she could accomplish the meagre task of making a simple cake.
Or die trying.
She knew that she'd have to get them out somehow and she had the feeling that the best way was by putting them all off so that nopony would want to go near her. She opened her mouth and poured more sickly-sweet sugar into it while giggling as madly as possible.
She narrowed her eyes, "Let's get down to business." she growled, but since her mouth was full of sugar, it came out as "Weth wet wown two buthineth." and she ended up spraying sugar crystals and spit everywhere.
"Eugh!" Chrysalis squealed, jumping back and out of range of Nightmare Moon's sugary spit, "I think I'm just going to go and do something else now. You won't want a cluttered atmosphere in the kitchen, I'll just get in the way." she turned and sprinted out before anypony could stop her.
"Sombra left bath running." Sombra mumbled, turning to shadow and vanishing through the air vents.
Discord sighed and shook his head, "Those two are the least enthusiastic of all, eh?" he said, "Well it looks like it's just you and me then to-"
"NO!" Nightmare Moon screeched, whirling around to face him, "I WILL NEVER LET YOU ASSIST ME IN THE DELICATE PROCESS OF MAKING CAKE!!!!!!!!!"
Discord held up his hands, "Fine, I'll just quietly sit over here and-"
Nightmare Moon was having none of that.
"I WILL NOT LET YOU 'SIT QUIETLY OVER HERE'! I CAN SEE IT IN YOUR DEVIOUS LITTLE EYES THAT YOU ARE RIGHT NOW PLOTTING ON MAKING ME FAIL MY TASK AND I WILL NEVER GIVE YOU THE SATISFACTION OF SEEING ME FAIL!!!!"
Discord sighed, "Right, fine. You got me, I was going to make you fail."
"AHAHAHA!!!!! YOU SEE, I AM THE NIGHTMARE, THE BRINGER OF DARKNESS AND YOU ARE A PRATTLING CREATURE THAT I CAN STOMP ON WITH MY MIGHTY HOOF! NOW I HEREBY BANISH YOU FROM THE KITCHEN UNTIL I FINISH MY QUEST OF THE MAKING OF THE CAKE!!!!!"
The draconequus looked offended, before he slunk out of the kitchen, sighing and muttering something along the lines of: 'talk about over dramatic'.
Nightmare Moon huffed a sigh and turned back to her mission.
Cake. Caaake. CaaaAaAAAAake.
Right, so cake. She needed cakey ingredients.
Caaaaaake.
Sugar, flour, coco powder, butter... What else?
Milk. Yes, she needed milk.
She walked over to the fridge and opened the door. She could see four unopened cartons of milk.
So far, so good.
She lifted one out with her magic and took it over to the bowl on ingredients. She unscrewed the lid and was about to pour some in when she was suddenly hit by a disgusting smell.
"Eugh..." she flinched back and then sniffed the milk in the carton. The idiots who lived in the house must have let it go off. She snorted, Peasants. She thought to herself as she poured the putrid milk down the sink.
She went back to the fridge and took out another carton of milk. She unscrewed it's lid and was just pouring it in when she was hit by the smell of sour milk.
"No!" she managed to catch the milk right before it hit her precious ingredients.
Nightmare moon glared at the carton and checked it's use-by date. It wasn't supposed to go off until three days and she suddenly got the feeling that Discord had been tampering with it.
"Alright then," she growled and poured the milk down the sink, "what are you doing this time?"
The Alicorn turned back to the fridge and her horn glowed dark blue as she cast a scanning spell on them.
"Aha!" she exclaimed triumphantly, "So somepony has been tampering with these!" she smirked, "Evidently, you are not clever enough to defeat me! Hahaha!" she cackled to herself as she basked in her cleverness.
Her blue aura wrapped around one of the last two cartons as she drew it out of the fridge and levitated it in front of her. She reached into it with her magic and to her delight, it hadn't gone bad. Smirking, she unscrewed the lid and then:
WHAM!
Instantly, she was hit by a foul stench.
Gagging, Nightmare Moon hurled the milk carton out the open kitchen window. So that's what Discord was playing at. He must have cast a spell that made the milk go bad the moment the lid was removed.
Well played, Discord. Well played.
Nightmare Moon gingerly lifted the milk out of the fridge as if it was prone to suddenly blowing up. As carefully as she possibly could, she began the delicate act of tinkering with the very atoms that made up the milk, reversing the spell on each of the particles that Discord had rigged up to cause the sped-up rotting procedure the moment the lid was removed.
The procedure was slow and painful, the Alicorn of darkness not daring to change too many atoms at one time. She had no idea how long she stood there, levitating the milk, tinkering with the particles and monitoring the cooling spell that she kept wrapped around the carton to make sure it didn't go bad naturally as she continued to reverse each and every bit of Discord's spell.
Finally, after what seemed like years (and may as well have been), every single bit of the spell had been cancelled and Nightmare Moon reigned victorious!
"Hahaha!!!" she laughed, "I have defeated you, Discord!" nothing could stand in her way! She was much more powerful than he would ever be!
She heard someone snort behind her and whirled around to see King Sombra by the pantry, trying to fit as many muffin bars as possible into his mouth. The Unicorn king mumbled something through his mouthful of unhealthy stuff and mumbled something that sounded a lot like 'weirdo' before shoving a hoof-full more into his mouth and trotting away.
Deciding that it would be cleverer to just ignore the insane mortal, Nightmare Moon went back to her quest. She used a measuring cup to add the exact correct amount of milk to her masterpiece before sighing with relief that nothing had blown up yet.
Now, what next?
"Baking soda." she whispered, her dark eyes wide as they wandered over to the cupboard where the ingredient was stored, "I need baking soda..."
She trotted over to the cupboard, wrapped her dark energy around it and threw the doors open.
BING-BOOM!
A jack-in-a-box popped out, bonked Nightmare Moon on the head before flying back in and slamming the doors shut.
The dark Alicorn stood there for a few seconds, staring at the closed doors with a stunned look on her regal face before tugging them open again with her magic.
BING-BOOM!
It flew out again and smacker her on the head again. She made a wild grab for it with her magic but the doors were closed before she could.
"Oh well played, Discord. Well played." she muttered darkly, "I see how it is. Well, you're going to have to try harder of you want me to fail."
Her horn glowed with magic as she gathered as much energy as she could before releasing a bolt of pure energy at the cupboard's doors, blasting a hole in the centre of the two doors where she had seen the jack-in-a-box disappear. It's head flopped pathetically out of the hole that had just been smashed through the doors and Nightmare Moon smirked.
Victory.
She strutted proudly over to the doors, wrenched them open and-
THWACK!
She reeled back, rubbing her head were a bruise was beginning to form. She instantly regretted leaving her helmet behind when she came to the house as she watched the mallet disappear like the jack-in-a-box back into the cupboard.
"Very well then, Discord." she snarled, "You're playing with the big mares now." even though there was no other mare, the line sounded cool.
Taking several steps back, she charged her magic into another energy blast. This one spread upon impact, completely destroying the cupboard's doors and took several chunks out of the wall surrounding it, too.
With the doors gone, Nightmare Moon could see all the devices that Discord had set up which got considerably more catastrophic with each trap. In the centre of the cupboard was a note that said, The baking soda's in the pantry, mule-head.
Nightmare Moon snarled in annoyance, "Well that would have been nice to know beforehoof." she muttered, stomping over to the pantry and taking out the baking soda. She made her way over to the bowl where she was mixing the ingredients and took out a spoon to measure the baking soda with.
Levitating it over the bowl, she opened the small container with her magic and at once, it tipped upside-down and poured all of it's contents in with the ingredients. Another note on the bottom of the container read: Haha, sucker!
Nightmare Moon stared at her ruined ingredients for several seconds. And then a piercing wail of pure, utter suffering tore through the air like a razor-sharp blade.
"So then," Nightmare Moon continued, "I threw it all out the window, tore all the doors off the fridge, panty and cupboards to make sure that there were no hidden traps, double-checked everything I used for magical tampering, ordered new baking soda and butter and started everything again." she looked proudly at the Changeling with her glittering eyes and matted and scorched mane.
Chrysalis nodded slowly, astounded by how far the dark Alicorn had gone to make a cake that Chrysalis couldn't eat, Discord would turn into something nasty and Sombra would mutilate. But being the extremely kind and responsible *cough cough* type of mare, the Changeling queen simply smiled and said, "I think you did great! Looks like you've passed Level One for Surviving This Household!" though she honestly doubted that Princess Luna's dark side could get anywhere past Level Two.
All the same, Nightmare Moon looked so incredibly pleased with herself, even Chrysalis didn't have the heart to tell her that within a few more hours, she was bound to be sent crying back to Princess Luna.
"Yes, I know, right?" Nightmare Moon said proudly, "There aren't many ponies as brave or skilled as me! For I am the Nightmare! The Bringer of the Night! The Yin to Celestia's Yang! The Hellfire at the end of the tunnel! The-"
She never got any further as all of a sudden, her magic that was holding up the cake was cut off and her pride and joy went splat against the living room carpet.
Deathly silence followed the Nightmare the Bringer of the Night, the Yin to Celestia's Yang, the Hellfire at the end of the tunnel, etc stared down at her ruined masterpiece with a look of complete and utter horror.
"Whoopsie." Discord laughed, popping up out of nowhere with an evil grin on his face, "My bad!"
Hurriedly mumbling an excuse, Chrysalis snatched up her fallen book and darted out of the living room, almost colliding with Sombra in the hall.
"Run."
That was all she needed to say. The Unicorn and the Changeling charged as far away as possible from the scene of the disaster as Nightmare Moon's terrible scream ripped through the house.
Author's Note
Based upon a time when I tried making cake... Though it didn't quite go this way 
