A Small Issue 3 - A Sight for Sore Eyes

by Lukington17

Rating: everyone
Tags: Discord, Slice of Life, Main 6, My Little Pony: Friendship is Magic, Spike, Science Fiction, Queen Chrysalis, Starlight Glimmer, Adventure
Length: 17337

Some changelings won't change - and they'll go to great lengths to prove it.

After the victory over the Eevies in their microscopic battle, Twilight Sparkle and Spike just want to relax for a while. But when Rainbow Dash gets an illness even the Doctor can't diagnose, the pair decide to investigate a little closer, and will have to use all the help they can get - even help from a higher power!

Cover art by Pen-and-paper

Published 2018-09-01 20:20:01 UTC
Last updated 2018-09-01 20:20:01 UTC

Chapter 2 - Troublesome Sight

Something has gone wrong. We don't seem to have an archived copy of that chapter.

Chapter 3 - A Rough Night

Twilight, fretting over Discord’s disappearance, had decided enough was enough. She was going to go in and find the conniving creep; she had been very clear about their plan. Twilight went up to her friend's guest room, to explain that she was going in after Discord, but was stopped in her tracks when she saw something happen to the blind pegasus on the bed in-front of her. For about a split second, her wings took on the form of changeling wings - it lasted a nanosecond, and Twilight told herself she was imagining things. However, she then saw closer-up that Rainbow had a black mark on her forehead - at least, she thought it was a mark. "Rainbow Dash, is your head okay?" She asked. Rainbow duly felt around her forehead and touched the strange mark.

"Aaaah Twilight, what the heck is that?!"

Twilight looked closer. "It...looks like the surface of a shell...how bizarre..."

Rainbow panicked: "Oh Celestia, am I turning into Tank?! Is this some sort of horrible curse where my pet and I swap forms? I've already lost my perfect sight like the old fella..."

"No Rainbow, I don't think it's that - but I want to find out what it is." Twilight tried to console her friend, and checked for a temperature that far exceeded a fever after her accidental chili-pepper ingestion. A frightened Rainbow put on her sunglasses in shame to hide her altered face as Twilight hugged her; the poor rainbow-maned pegasus felt completely broken, humiliated and shaking back-and-forth in fear. She turned to Twilight and started sobbing, “Twilight, what if the eyesight never comes back? What would the Wonderbolts do to us?! Please… PLEASE let us see again, Twilight!” Twilight sat sadly at her friend’s side, until she realised something. ’us’? Why would she refer to herself as ‘us’?. Immediately, Twilight understood what was happening. This was a last-resort SOS, coming direct from Rainbow’s brain…as controlled by somepony within, with a voicebox over-ride. She tried to calm her friend once more, but couldn't get out of her head the image of Rainbow's changeling wings, and how her faded eyes had turned blue.

"Don't you worry, Rainbow Dash...hold still. Whatever has happened to Discord, I assure you I won't let it happen to me. No one knows you like I do." The friends smiled at each other, although Twilight knew there was a whole micro-civilisation who would argue that they knew Rainbow better than her. Smirking to herself, Twilight applied the newly-developed Zeromac and flew rapidly up into Rainbow Dash’s nostril.

“Ugh”, the sunglassed Rainbow Dash sniffed, rubbing her nose.

Unbeknown to Rainbow, Spike and Starlight Glimmer had been lurking outside the doors. They had been listening intently amid concerns for their friend. Of course, Spike knew where Twilight was going now, and was eager to help her again. He couldn't just leave Starlight in the dark now about what was going on; she might even want to help. He turned to her and explained about Zeromac and their previous adventures. "...So you see, we have to venture inside Rainbow Dash’s body, because if we can’t fix it from the outside…”

“…You’ll fix it from the inside.” Starlight finished the thought, and stroked her chin.

Spike replied, "Exactly - you should come too though!" Starlight gasped, but he pressed on: "Think of it as a major scientific study for you. Twilight will be so touched that you came in to help! And soon I’ll be more of a hero there than I am in the Crystal Empire!”

Starlight thought about it, and eventually smiled. Spike added, "You’ll surely have a stronger stomach than Rarity, she couldn’t really handle it.”

With a wink, Starlight replied: “Let’s hope Rainbow’s stomach can handle me!”

The duo headed quietly over to the desk, beside the couch where Rainbow was now sleeping loudly. On the desk remained a remnant of the Zeromac which Twilight had left behind, a vague attempt to cover it having been made by a few loose sheets of paper and letters. They moved over to the couch, leering over the snoring Rainbow, and huddled up together as Starlight used her magic to pour the potion over the two of them, measuring the amount from the marker Twilight had etched into the beaker. Instantly they felt a weird sensation - the sort of head-rush felt from orthostatic hypotension when getting up too fast - and Starlight even screamed in fear. Terrified that she’d woken up Rainbow Dash and given themselves away, she zipped her mouth shut immediately as Spike held a hoof to her mouth. It was only when all was quiet that they took in their surroundings.

The entire room was still there, but it went far, FAR beyond their eyes could see. In fact, the roof might as well have been outer space. The walls and curtains raised high up into the heavens, and they could make out all the particles of dirt and dust around them. “Woooah” Starlight exclaimed, “Where are we?” They looked down: the surface was soft and made of felt, but each lump of the felt was almost a thousand times the size for them now, the size of a sofa. And that’s when they realised where they were: the sofa. To be precise, they were perched on the top of the sofa’s backrest, and swooping down their horizon led them to their goal: Rainbow Dash’s face. Her enormous head was resting on a cushion right below them, facing upright, her glorious rainbow-mane flowing over her muzzle slightly, sunglasses still intact. The shrunken pair could practically make out their reflections in the gleaming blackened glass. The pair held each other tight and braced themselves. Spike looked down with excessive excitement as Rainbow’s immense mouth opened wide - he was sure one of her teeth looked oddly sharper than usual - and it let out a snore. The soundwaves practically shattered their ear-drums this close - and besides the faint smell of spice left in their noses, their ears were ringing as they hurled themselves down the sofa.

Starlight grimaced in fear and hesitation; Spike rolled his eyes at her as the inhale from the mouth allowed for them to be dragged on-target, falling into Rainbow Dash’s mouth as the uvula wiggled teasingly at the back with the intake snore.

“Are you okay?” Spike asked, as they picked themselves up from a rather bumpy landing. And boy was it bumpy: all around them, massive lumps of pink soared upwards into the dark sky. The ground below them shook and shifted upwards slightly as gusts of air whooshed over their heads.

“Just about…” Starlight steadied herself and took in the surroundings; now in a more closed space, their view was slightly improved. They were standing on the tongue, having landed on it as it curled in a favourable way for them. To either side, the enormous molars – which still took up most of their view – acted like pivots of the jaws in front, which hung open and allowed the light of the outside room to pour in. The jagged lines of Rainbow’s front teeth acted like a frame for this view outside. “Amazing…” Starlight thought aloud, marvelling at these sights, and then wincing when she noticed some dark staining and cracks on a few teeth. Yikes, she may be awesome on the outside but I think she needs to see an awesome dentist... she thought to herself. With saliva dripping from her wet hooves as she moved, she turned to Spike. “Eeww…okay then, where in tarnation are these tiny ponies you were so excited about? I knew there couldn’t be such thing as a microscopic city – no organisms could sustainably construct an artificial habitat in the conditions of the -"

“Freeze! Don’t move!” Came a gravelly voice from somewhere behind. The pair stood absolutely still in fear. “You have entered the City of Rainbow Dash,” it continued, “and as unauthorised entrants, are required to present proper documentation.” The speaker eventually revealed himself, a shabby-looking brown pegasus stallion wearing a hardhat and hi-vis, accompanied by two other pegasi behind him. The pair noticed the trio's uniforms were labelled BORDERS – MSD DIVISION , but they blushed innocently and held up their arms, unable to show any documents. “Right, you’re coming with us…” the brown stallion said, and the workers hoof-cuffed the pair and picked them up, heading along the tongue’s surface to the back of the throat. It was noticeable how the loudness of Rainbow’s snores seemed to be drowned out here, almost muffled and somehow contained. As they flew along the surface, Starlight saw a team of four tiny ponies having an argument around several sore taste-bud that had various incisions in them.

“I told you that wasn’t going to work!”

“You never said that – all you did was act all high and mighty without offering any suggestions”

“Well don’t you start, you said that lingual papillae were the easiest to fix!”

“Don’t look at me, I’m not the one who’s supposed to be from Spice Control…”

“Oh yeah? I’m just from Enamel Care, how do you think I feel?!”

Amused and still shocked by the discovery of these microscopic pony organisms, Starlight sniggered, in spite of their situation. Spike's recounting of the tale had been rushed and so it was all a lot for her to take in! The stallions now soared up away from the tongue, heading towards the uvula suspended high up in the throat, like a starship lingering ominously in space. Indeed, as they got closer, the control centre on its base came more into view, indeed looking like an under-hanging spaceship attached into the uvula’s flesh. A bright red beacon flashed regularly off the lowest pole on the apparatus. Eventually, the stallions carried them to a gangway and led them through the doors at its end. After a lengthy walk through various offices and elevator rides, they reached the round and grand observation platform-deck, with its glass panels swooping around almost entirely in a circle. This room was the busiest so far, with various ponies in lab-coats running around and taking notes at the monitors dotted around the room. Spike realised that, as well as being slightly hot and muggy in here, none of the lights in this room were on; it was relying solely on the outside light shining into the open mouth.

A beige mare turned around from her chair and walked towards them. “Release them,” she demanded, and with a huff the stallions untied the duo and walked out the room.

“Spike, how nice to see you again. And this must be the new friend of you and Twilight. Pleased to meet you, welcome to the City of Rainbow Dash! My name is Oovla, I’m the Head of the Mouth Sanitation Department here in the Mouth & Throat District. We were expecting Twilight in the city today but not you two fine visitors.”

“Pleased to meet you, ma’am” Starlight said with a respective bow of the head.

“I’m afraid you’ve arrived at a very bad time, Spike. The city is suffering a blackout, and much of our equipment has been affected.”

The dragon looked saddened, but then Starlight noted: “I saw some ponies fighting on Rainbow Dash’s tongue.”

Oovla let out a slight smile. “Yes, well – for whatever reason, City Hall authorised consumption of a chilli pepper which we weren’t prepared for at all here. There were fires around the city because of the heat, but the taste-buds here suffered badly, and I’ve had to ask some of our Dental Hygiene Unit to help us repair the buds’ damage – those things are sensitive, you know!”

The pair looked puzzled. “How can such chaos be happening?” Spike asked. “Surely someone or something is responsible…Discord…”

“No, it’s not Discord. In fact, he was apparently seen in the Brain trying to interrogate pedestrians.”

“Pede- why?” Spike looked puzzled.

“We have a changeling infestation.” Oovla sighed after the dramatic reveal, and the pair gasped.

"Oovla, we have to find Discord – and Twilight! She’s supposed to be helping here too!” Starlight said determinedly. “Which way to the Brain?”

Oovla hushed them and handed them both VIP passes from her desk, warning them to keep those visible. She then summoned some pegasi workers to escort them to the Brain. “Take these lovely visitors to the Brain if you can. Go quickly; we have to prepare for a yawn here in 2 minutes.” As if on cue, a countdown timer announced this fact. The pair thanked Oovla and then the waiting pegasi lifted them up once again, allowing them to ride on their strong backs as they flew with torch-fitted hardhats. Apart from the streaks of the torches' lights, the sights were all lost in darkness: all that the pair could make out in the dim city were the imposing silhouettes of buildings against the various walls of Rainbow’s body; the nervous transit system lay dormant, its flowing pipes and tubes no longer illuminated and filled with the sounds of rushing vehicles. In an effort to get a better sense of this place, Starlight used her horn to illuminate their path better, showing the buildings around their brightened radius. Spike was reminded of his last visit here, when he and Scootaloo had bonded over the fun urban exploring. He felt an immense sadness come over him, only imagining the pain and confusion that Scootaloo's idol must be experiencing outside. As they passed by some foreboding grey structures, they heard their voices being called desperately.

“Spiiiiiiiiiiiiike! Starlight Gliiiiiimer!”

“Wait!” Spike haulted their escorts, and headed towards the outlines of a gate in the darkness. The pegasi aimed their torches at the gate to show that they were at the Correctional Institute. The voice called out once again, and the four of them noticed a small light flashing from a window.

“It’s me - Discord! Get me oooout!”

Spike gasped. “It’s Discord! We’ve gotta find him – hold on, Discord, we’re coming!” The candle-lit security guard saw their passes and opened the gate, guiding them to the cell Discord was detained in. The MSD pegasi had to return to their posts back in Rainbow's mouth, so they left the pair here. A changeling guard strolled on a walkway above them with a flashlight, and Starlight gasped at this sight. Trying not to get scared, she peered into the cell lit by her magic, and Spike held her tight. The draconequus sat looking rather dejected.

“I failed Twilight, I was supposed to come in and help and in reality, all I am is damn useless…” he grumbled remorsefully, but the pair helped him up and led him out his cell.

“Come on, we’re getting outta here, Discord” Spike said, checking the coast was clear. "I wish I had Thorax with me..." he added, remembering the changelings' reformation he had pioneered as he considered the evil changelings he had seen in here. For now, the changeling guard had vanished, so they hurried out through the darkness as fast as they could, using the darkness to their advantage as they zoomed past the gates unnoticed. Once they felt they had travelled far enough from the prison, they stopped and caught their breath. It was still incredibly humid where they were.

“Discord…” Starlight panted, “You are one of the most important folk around here right now! You’ve been here before, right? You know this place like the back of your…hand, claw…? Now show us the way to City Hall and let’s give Twilight the help we know we can all give her!”

“And kick some changeling butt!” Spike added, even making Discord smile now. He then proceeded to pull out a faded map of the cellular city, shining his little flashlight on it and leading them to one side.

Twilight had entered the nostril before Spike and Starlight had walked into the room, and had found almost immediately that not only was something not right; she couldn’t even see! The nasal passage’s highways, usually illuminated by bright streetlamps soaring high above the traffic, were all but imposing shadows and monstrous outlines curving and rising over and around the snotty surface on which this was all built. Using her horn to illuminate the way, she had managed to navigate her way further down the passageway, eventually heading past the sinuses and Olfactory Bulb, and arriving in what felt like a big, open space. Suddenly her lit horn did not seem to cover that much area, and although a few tiny dimly-lit lights appeared off in the distance somewhere, the inky blackness immediately surrounding her made her very nervous. This doesn’t feel right...clearly there’s been a power-cut across the city. Pretty serious. She thought to herself, trying to calm herself a bit. Her attempt was short-lived, as she suddenly became very aware that she was being watched.
"Yaaaaaaaah!" She screamed as she felt some unseen force grab her leg and drag her off to one side. The sound of a familiar sinister laugh echoed around her - and upon seeing a pair of green eyes in the darkness, she yelled out. "Chrysalis - I know it's you! Reveal yourself!"

The changeling queen stepped out of the shadow and basked in the glow of her horn's eerie light. "Well aren't you a sight for sore eyes," she chuckled. "Funny, isn't it? A changeling spell can still work at this size."

Twilight wrestled the unseen force that was still pinning her down. "N-no...impossible...what are you on about this time?!"

Chrysalis growled and gestured to two more changelings who appeared, holding down Twilight as the queen leaned in to her. "You and your damn ‘friendships’ have thwarted me too many times, I will fight these friendships one-by-one by turning them into the very thing you overthrew!"

Twilight gasped as she began to piece together a horrific picture. "Surely you don't mean..."

Chrysalis cut her off, perhaps consumed by pride and arrogance: "Of course I do. The other day I found an ancient Changeling Spellbook in a deserted castle formerly belonging to one of my predecessors, out in the barren lands, and found in it a spell which can conjure changeling ‘essence’, energy, from one organism to another, bit-by-bit."

Twilight interrupted, "You have a spell that can transfer Changeling energy to any organism, even at this tiny size? A spell which can turn cells into changeling cells?!”

Chrysalis laughed. "Just look around you! Even these two here, formerly of the RDFD and one from the Spleen. Now they are mine!" Twilight moved to protest, but the self-absorbed queen continued: "I might as well tell you since you will not be interfering with my plan this time, Twilight Sparkle. I will see to it. With the spell perfected I then decided to target one of your closest friends, Rainbow Dash, with the intention of applying this spell from within. Obtaining that stupid shrinking potion in the Canterlot labs was easy; those guards didn’t suspect a thing from ‘Luna’. What I didn’t suspect was an entire city of microscopic citizens in here! This discovery, however, makes things a lot more interesting…yes, I have most certainly used this to my advantage.”

Twilight tried to wriggle free in vain: "What are you going to do to my friend! Leave her out of this, your issue is with me!"

Chrysalis laughed as she began to walk off: "Oh Twilight Sparkle, this isn't just some small issue between you and I anymore. No, I've been caused enough grief. And soon, there won't be a 'you and I' anymore! Mwahaha!" Her laughs faded as she disappeared into the darkness - but the changelings holding her suddenly picked her up and headed off somewhere. They glared at her as she shifted around in their grasp, but they did not break their stride – they both seemed rather strong. They were using a similar illumination spell, as Twilight could see after a while through their light that they were on Ureter Avenue – she was confused and began to shift around uncontrollably in the grip of the changelings. “Let me go! Get your dirty hooves OFF me!” Around this time, they were nearly blinded as almost every light in the city came on at once. “Aaaoooow!” she and the changelings cried as their sensitive eyes were burned with the brightness, and all around them various citizens moaned in similar pain as they began to emerge from their respective homes, vehicles and hiding places. They were all too busy to notice the changelings drag Twilight down a side passage marked 'URETHRA (Sanitation Department Staff only) - STRICTLY NO ADMITTANCE'. The changelings were muttering about how ‘they must have fixed one of the eyes’. Confused by this, Twilight - still rubbing her eyes - realised they were in a narrow shoot, and had now been joined by another changeling – and also a micropony! Surely they weren’t causing citizens to be defecting?! They stopped at a small platform, with a control panel to one side – and an immense drop below it, leading down to a vast river of… well, Twilight knew they were in the Urinary Passage, not just by the smell. This immense tunnel seemed to be channelling the waste fluids down, and practically right below their platform, the river suddenly dropped – indeed, there was a large waterfall where the cascades descended into the external sphincter of the urethra. The sound of gushing waters filled their ears as it tumbled downwards, and the four captors tied string around Twilight’s wings. It was a very humid and damp climate in here, and all five of them struggled to conceal their sweating.

“Right, off you go!” One of the changelings prodded her to jump.

Twilight tried to use her magic, but the changelings rebuffed it almost immediately with counter spells. With tears in her eyes, she turned to the micropony. “H-how could you? This is your city, how could you let it crumble before you?”

The micropony sniggered and revealed itself to be nothing more than a changeling, albeit in a convincing disguise. Twilight gasped and then tried to formulate a plan quickly. Smiling to herself, she asked: “Say, do I get a last request?”

“Fine.”

“I would like an ice cream.”

Some of them sniggered. “An ice cream?! From where?”

“Oh I sorta want an ice cream now she’s said it…”

Twilight stayed calm: “down there, can’t you see there’s a vendor right there?”

“Huh?” All four of the changelings peered over the ledge down to the bottom, and Twilight seized all her power and might to wallop their backsides in one go, knocking the surprised quartert over the railing and plunging into the waters. “Uuuugh! Gross!” They cried, trying in vain to flap their inferior wings. Due to the sweaty conditions, and their soaked bodies from the waste fluid, they were unable to propel themselves out, and tumbled over the edge and down the waterfall, screaming out in anger. Twilight sighed with relief as their shouts faded away, and then she turned to the control panel, shaking her ropes off. A bright green button had a picture of Rainbow Dash’s body outline with an arrow pointing out from her nether regions. Shrugging amusedly, Twilight pushed the button and looked down below as a whirlpool began to drain the pool at the bottom.

--- “Aaaaw, man!” Rainbow Dash groaned as she was awoken by a sudden need to use the toilet, and sleepily stumbled over to the bathroom, too tired to realise she had regained her sight.---

Twilight charged back up the passageway and into Ureter Avenue. She headed up towards the kidneys and recalled that the last time she was in this city, she had made a new friend in this district. She flew as fast as she could through the city, heading back towards the brain via the spinal cord. She flew along the highway and soon enough passed a sign marked “Exit 74 - Neck Hill North”. She knew she was nearly there, but at this moment she was suddenly pulled off the freeway and sent tumbling into somepony. “Hey, what’s the big de-“ Twilight stopped as she realised she had crashed into Starlight Glimmer, Spike and Discord. “W-wha?! Am I going crazy now?"

Starlight sniggered and hushed her friend. “Sorry, I guess I yanked you outta there a little hard. Spike was adamant we should come and help you, I couldn't say no." Twilight looked at Spike, initially with a frown but then a heartfelt and accepting smile. Starlight continued, "We were waiting here for ages hoping we’d see you on the main highway. How are you, what in Equestria happened?!”

"It's Chrysalis - she's somehow found a spell which can turn the cells here into changeling cells, one by one! It seems they're already affecting Rainbow's appearance on the outside now...Chrysalis is clearly trying to change every cell here which would mean that Rainbow altogether would become a..." She paused as she realised the horror of Chrysalis' evil plan, thinking also of how she threatened to attack all her friends. "We have to stop Chrysalis; it won't be long before she reaches the Brain, where she'll be able to 'install' the changeling ability to morph - if she does that, I fear we may lose Rainbow for good!"

Starlight and Discord exchanged glances and recalled the time they had overcome Chrysalis to save Equestria, so Starlight gave her friend Twilight a confident look. "Don't worry, Twilight - we're here for you. We'll kick Chrysalis back where she came from, 'cos we're here to help. Are you okay though, where have you been?" Twilight recounted her escapade inside Rainbow’s bladder, and Spike couldn’t help but laugh at the gross ending for the captors. Twilight then shot a furious glare at Discord, about to lash into him - but Starlight explained: “Wait, don't attack him. Spike and I were taken into the MSD office in Rainbow's uvula when we came in. As we were heading to find you, we found Discord in a prison, hence his lack of communication…we rescued him though! This place is amazing! It’s like…a groundbreaking scientific discovery! We have to share it with the Canterlo-“

Twilight booped her friend’s mouth shut. “Nopony’s sharing anything, certainly not until we figure out how to save this cellular city. Rainbow's life as she knows it depends on us now."

Spike spoke up: “Twilight, we bumped into an old friend you should come and see…”

Twilight gasped, “You saw her?!” Twilight's worst fears flew round her head: Have I just been tricked by the damn changelings? Did I just escape for nothing? Are all three of my friends here just illusions, changelings in disguise? After Starlight shook her head and reassured her it wasn't a betrayal, Twilight looked excited. “Oooo is it Minuette? Moondancer?” Spike shook his head and they led Twilight into Neck Hill, the affluent district for the rich and elite citizens. A lot of politicians lived around here too, being so near City Hall. They rang a doorbell at a rather impressive mansion, waiting until a familiar face answered. “Action Tremor!” Twilight wrapped her arms around the stallion, who smiled as he hugged her back. The former Mayor welcomed Twilight as Starlight and Spike followed in with Discord.

“Woah, this is much nicer than that old barge down in the bloodstream!” Spike remarked, receiving a stare from Twilight. After having a pleasant catch-up over tea, they overheard on the television that the Optic Nerve Highway had been completed after emergency sectioned back-up lighting was authorised by City Hall, and that Rainbow Dash had been taken to Zecora’s Hut by her friend Fluttershy. Their host was still suffering from slight delusion after the blackout, and the Department of Vision was depleted still. At least the sections of carapace had been successfully removed by an RDFD team.
They then tuned into a slightly wonky RainbowVision and observed as Rainbow herself wearily observed the strange décor of the hut, ranging from medicine bottles to frightening tiki masks.

At this point Twilight had a sudden thought, having grown in anxiety over the developing changeling epidemic spreading through the city. “Action Tremor – is there a way of actively controlling Rainbow Dash’s dreams? I have an idea.”

Action Tremor nodded slowly. “Sure, the Memory Department. Been a while since I set hoof in there; I’ll have to see if I can get us in.” They presently headed off for Brain Central, Action Tremor driving them in his luxury cellular car. They headed towards the Memory Department, which was a large and dark-coloured office block on one side of a quiet square off one side of the main plaza, incorporating a Bank and cinema opposite. They parked and headed into the governmental office reception, unaware that all around the plaza, changelings were lurking on the sidewalks and gesturing to one another to slowly encircle the building. After murmuring at the desk with the deadpan mares behind it, Action Tremor smiled and gave a smile of encouragement to his waiting friends. They rode an elevator several storeys, coming out in a dark corridor and walking down it. Numerous closed doors on either side of them seemed to have light coming out from under them, with muffled sounds of clips and reels apparently being screened within them. Twilight and Spike were reminded of their first venture into the city, when Discord had tricked them into starting a fight in the department cinema’s screening room of Rainbow Dash’s dream that night. Now however, Discord was behaving behind them and they were being taken to the ‘control room’ studio.

They entered the large room, full of control panels, monitors and cameras everywhere, and two microponies so engrossed in their work that they didn’t even stop to look at the newcomers. Action Tremor explained: “This is the control room here at the Memory Department. Here is where the dreams themselves are constructed, before being sent to the cinema for screening. As you can see, it takes a lot of meticulous planning to make sure we get the dream exactly right and fuse the right memories together, allowing for some…imaginative creativity I suppose.” The gang watched as the microponies busied themselves with all sorts of documents and files, talking into their earpieces. Fluttershy and Zecora had tucked Rainbow in bed and so she was actually sleeping now, so this was a relatively quiet period since the dreams had already been dispatched for the night.

Twilight approached one of the workers and struck up a casual and friendly conversation, eventually prying with a bold request: “Is there any way you would be so kind as to let us over-ride tonight’s dream? It’s urgent - the city is in grave danger and I need to infiltrate the dream.” The worker looked in disbelief, so she pressed: “need I remind you that I am Princess Twilight Sparkle, Rainbow’s friend.” The worker hurriedly grabbed his co-worker and Action Tremor.

“Little Miss Sparkle here wants to over-ride the dream. Can we even DO that?”

“Yeah who cares, Cody - just do it.”

Twilight squeed happily as she was shown how the machinery worked, and a message was relayed to the cinema to halt their screening. She looked visibly excited to be exposed to new scientific apparatus – she then mustered her magic and focused long and hard, as the assembling camera-crew and workers watched on from various doorways. She moaned in pain as her horn glowed brighter and brighter in a white glow. Eventually, Twilight zapped the console and a stream of white flowed into it, appearing on the monitor. When Spike nervously asked what she’d done, she explained quietly: “I remember Princess Luna showing me how Rainbow loves to kick ass in her dreams – not sing with sunflowers, remember? So I’ve initiated a dream sequence for Rainbow which will bring her into this city to kick changeling ass!”

Spike stared open-mouthed. “Are…you…nuts?! What are you thinking?”

Twilight had that worrying look of excitement mixed with crazed perseverance, perhaps an adrenalin rush caused by the spell. “Isn’t it great?!” She exclaimed. “I’ve managed to create a spell which breaks the laws of physics – she’ll be inside her own head! I should get down to the square, she’ll be here any minute!” Spike and Starlight were helpless to stop her as she zapped herself out of the room, and the crew all shrugged and looked as the monitor showed Rainbow’s eyes slowly waking up to a very familiar location.

Rainbow Dash rubbed her eyes slightly as she slowly adjusted to her surroundings. “Huh? What’s going on?”

“Hi Rainbow Dash!” Twilight flew towards her.

“T-Twilight?!”

"Yeah! Look out, changeling at 2 o'clock!"

"Huh?" Rainbow turned and saw two changelings advance towards her in the square, and she proceeded to kick them away and punch them in typical Rainbow Dash awesomeness. Twilight pointed at more changelings incoming, and again Rainbow kicked and threw punches, banged heads and eventually a pile of defeated changelings had risen higher than a building nearby.

"Yeah! Woooo!" The cheers erupted from the studio and also the cinema nearby, as the citizens watched the unfolding events of their own host making history, despite her complete ignorance of it for the moment.

Rainbow continued kicking changeling ass until with an almighty bang of the head she knocked the last one out cold. The entire place shook slightly for some reason, and as Rainbow rubbed her head she sat down and panted. "Whew...we're safe now, Twilight! Where even are we?"

“Look around, silly! Welcome to your brain!” The alicorn had a deranged tone in her voice that betrayed the friendly expression she wore.

“My what?” Rainbow looked around properly and gasped. An enormous brain soared high above her eyes in the distance, electricity flying out of it high above. Down here between her and the brain, there were buildings of strange cellular matter, gelatinous ponies walking around the large plaza they were now stood in. She shook her head and chuckled with sarcastic amusement. “Haha very good, Twilight, nice joke. You might be trying to pull the wool over my eyes, but I’m not blind anymore… I sent you up my nose to cure me, not to play pranks on me.”

As she laughed at Twilight’s apparent ‘joke’, Starlight and Spike had managed to catch up to them in the plaza. Action Tremor and the crew of the Memory Department were watching from the studio in disbelief. “I’m sorry, Rainbow Dash – but this is no joke.” Twilight said, suddenly adopting a serious tone; by now Discord had joined them.

“This really is the inside of your head,” Starlight added, as Spike nodded.

Rainbow looked around again, stopping her laughter: a young newspaper-colt shouted the headline ‘Rainbow Dash taken to witchdoctor’; businessponies deep in conversation headed into the grand entrance of a building marked CITY HALL at the base of the brain; posters on a bus stop with her own face on them; television monitors in a shop talking about ‘fine weather forecast for the stomach’s beachgoers tomorrow, lunch-permitting’; a ‘dream cinema’ to one side; and, right in the centre of it all, a large statue of herself with the plaque: “Rainbow Dash: our city, the perfect specimen”! As she stood stupefied, a few microponies noticed her and began to gather around her, including several rushing out of the cinema for some reason. Even the news anchors on the monitors seemed to have stopped talking to watch somehow.

“Is that…?”

“It can’t be…”

“How can she even…”

And even a rambunctious young colt ran to her: “I never thought I’d meet you, please sign my pet globule! I’m Tubette from your colon!”

Rainbow Dash was panting in fear, panicking, until she let out a yell and tried to run away; Twilight went after her. “Rainbow Dash, these citizens are counting on you – I know you love to beat up changelings in your dreams, so I thought-“ her words were not listened to however, as the freaked-out Rainbow crash-landed, overcome with fear and disillusion.
Distorted images of these strange cellular ponies’ faces began to infuse with tiki masks and changelings that laughed at her tauntingly. She cried out and begged for it to stop, shaking her head in denial and curling up in tears, refusing it to be possible. Twilight saw this and snapped out of her own delusional mindset. “Oh sweet Celestia, what have I done?!” As Starlight and Spike were torn with what to do about their dejected and traumatised friend, Twilight flew back to the studio and shouted to the crew.

“Snap her out of it, snap her out of it now! Get her out of here!” Almost in tears, she bellowed her order to anypony who would listen – Action Tremor had to shake himself out of a state of disbelief at what he’d just witnessed, and ordered the crew to end the dream immediately. Sure enough, the cameras switched off, the monitors went black, and Rainbow Dash instantly disappeared from the spot she was curled up in. As everything calmed down for a minute quietly, the whole city seemed in a state of bewilderment. Echoing from the monitors dotted around, a news anchor bravely spoke up and continued his news casting: ”We interrupt this story to provide some breaking news: Rainbow Dash has just entered…Rainbow Dash! Yes, our host has just been seen in Brain Central plaza, attracting crowds of-“ “Turn that off,” Twilight interrupted, and the screens in the studio were duly shut off. “Great” she muttered sadly, “now everypony will know about my huge mistake.”

Action Tremor put a hoof on her shoulder. “Not necessarily,” he offered. “We’ve had bad dreams here in the past. There is a way to eradicate such problems.” Twilight looked up at him with the faintest of smiles, and he in turn spoke to two workers near the back. “Harris, Clemence – you know what to do. Code violet.” The two microponies scuttled off, and Action Tremor explained to Twilight: “they are going to fog up the memory of the dream. If it’s successful, it should generate a shockwave through the city that removes it from even our own recollections, not just Rainbow's. It’s something we only ever do in an extreme emergency – but I think we can all agree that THAT was as much of an emergency as we’ll ever get.” A few ponies nodded, and Twilight managed a smile of thanks as the workers hesitantly got back to work. Twilight wanted to cause no more damage, and so they left the building with Action Tremor and the four of them stood in the square. A couple of minutes later, there was indeed a red warning light flashed across the square, and a large wave of purple surged through them all.

“Are you okay, Rainbow Dash? I heard you shouting.”

“Ugh, I think I’m okay Fluttershy, thanks. I had a nasty dream and it just woke me up” Rainbow rubbed her head slowly. “Can’t remember what happened, that’s weird…I just had it. Oh well – good, I guess.”

Fluttershy looked nervous, “oh dear, whatever illness you have, it seems to be sneaking into your subconscious, Rainbow Dash.” With that, she headed out the door.

Rainbow scowled and turned in her bed, thinking to herself well DO something about it!. As she tossed and turned in her bed, struggling to get back to sleep, images flashed through her mind as she muttered to herself. “Ugh….brains…statues….”

Twilight Sparkle ran straight back into the Memory Department after watching Rainbow begin to piece her dream together on RainbowVision. She stormed into the studio and shouted: “Harris and Clemence, where are they?!”

“We’re right here, Twilight Sparkle” the two of them replied in monotonous voices, almost zombified in their posture.

Twilight bore down on them. “Are you NUTS?! What kind of job do you call that? You clearly aren’t wearing the uniforms you deserve…”

“You’re right, we don’t…” And with that, they both transformed before her eyes into the sniggering changelings who’d stolen the identities. “Unlucky, Twilight Sparkle. It seems your mistakes are gonna cost you this time.”

“No!” Twilight dodged their incoming grasps to capture her, and fighting back the tears she ran out the building, sitting on a bench and hiding her face. Spike found her and perched next to her; she told him about the infiltrated workers.

"It's okay, Twilight. Somepony will properly remove the dream from her memory - maybe not today, maybe not tomorrow, but soon enough that this will all be forgotten. We need you though, Twilight. Come on, don't give up just yet. Look, Starlight came all this way just to show you how much it means to her that we work together to help our friend get better!"

Twilight sniffled and looked up. "I suppose...this is only a mistake if I choose to make it a mistake...I can still get Rainbow to help us, I know it. I might have screwed up on my methods, but something tells me there is a way." Spike hugged her as the two sat, watching the citizens slowly recommence their daily activities.

Chapter 4 - Lost In Your Thoughts

The gang were trying to get some sort of reaction out of Twilight, but she simply stared off into the distance and offered little sign of mental stability at this point. In fact, her eye twitched slightly and Spike noticed her lips moving a tiny bit; she was muttering to herself. Action Tremor informed her that the Memory Dpt. were working on re-erasing the bad dream, but it got no reaction from the alicorn. Just as Spike was about to poke her, she suddenly turned and addressed them all, sending the dragon reeling backwards in surprise. “Listen to me. I can’t pretend to be okay because I’m not. I just did something incredibly reckless, and now I need to put it right. I’m not used to my plans backfiring, everypony – I feel like I’ve let you down, I’ve let Rainbow Dash down, and I’ve let myself down.” Starlight moved to console her, but she waved it away and continued: “I may have made a mistake in summoning Rainbow into a world she was not ready for yet. However, I might be of sound mind. Look - Chrysalis is out there with an evil plan, and we need to stop it. I know Rainbow could help us help her…so, I need to do something. First, I need to make sure Chrysalis is in this city and only in this city.”

Discord remained tight-lipped but Action Tremor spoke: “What are you gonna do, Twilight?”

Twilight gave him a reassuring smile. “I have to…try something. On myself. Stand back.” As the group backed away, Twilight conjured up her magic, summoning all sorts of glows and auras around her body as she suddenly enveloped herself in a bright white glow. When the glow faded away, the group looked puzzled as Twilight still remained there, but static – she was like a robot, dormant and motionless, gazing off into the distance.

“What did she do?” Action Tremor asked.

“Twilight? Can you hear us?” Starlight prodded the alicorn.

Spike pieced things together: “Hang on guys – that was almost the exact same spell that Twilight used to bring Rainbow inside her own head…so that must mean…”

“Twilight has gone inside her own head!” Discord suddenly exclaimed, then apologising for his outburst as a few passers-by gave him a weird look.

The others nodded slowly as they stared at Twilight’s unresponsive body. “Wow, inside a brain whilst inside a brain…that’s Twilight alright” Spike sighed. Carrying Twilight with them, they headed into an abandoned cafe having decided to take cover from the lurking changelings.

Twilight, meanwhile, had cast the spell on herself partly out of guilt, partly out of duty, and partly due to her scientific curiosity. She had been plunged into a void of bright lights coming from all directions, unable to keep her eyes open from the bright light she seemed to head towards. At this moment, she collected her thoughts. What if Chrysalis has already contaminated my own body? How will I overcome the dilemma of internal conflicts and win over myself, the way poor Rainbow Dash failed to do just now? If I can do that, perhaps I can then use it to get Rainbow’s cooperation, possibly without her ever knowing...? She was snapped out of her thoughts, as in a sudden flash everything went quiet, and she opened her eyes cautiously.

She looked up and saw an immense brain, again buzzing with electricity near its summit, and all sorts of veins and nerves shooting off. Something was wrong. There was no City Hall at its base. Curious, she looked around more, turning on the spot. There was nothing but a vast expanse of matter, cellular shapes moving around past her; there were no protoplasmic buildings, no microponies walking around. Everything seemed as her biology books from elementary school had told her: empty biological structure, organs and anatomical matter all in check. She couldn’t help but feel disappointed. Are these micro-civilisations selective on their domains, only settling in a few bodies? She knew for a fact that both Rainbow Dash and Pinkie Pie unknowingly hosted internal cities, yet hers was completely empty and void of ‘life’! How could this be? The only thing she could not account for was the inexplicable light which illuminated this cerebral locale. Giving up hope, she turned and took a few steps as she craned her neck to observe one last time. Did I do something wrong with the spell? How come it worked with Dashie? As she took another step, she suddenly felt something bump into her – something that moved, and something that made a gasp. “Whaa?!” Twilight exclaimed. “Who’s there?”

Right on cue, and to Twilight’s disbelief, a micropony suddenly manifested herself, coming out of some form of camouflaged spell in an almost pixelated manner. “A changeling, I knew it!” Twilight yelled in a rage, and moved to attack the pony, but she cowered before the princess and pleaded.

“Please don’t hurt me, Princess Twilight! I’m not a changeling!”

“How can I tell?”

“Um…the first thing you ever fed Spike was the trapiche emerald from your gemstone collection!”

Twilight reeled back in shock. That was a fact that only she and Spike could have possibly known. “Oh sweet Celestia…then that means you’re…there’s a…”

“Yup” the mare stood up, and shook Twilight’s hoof. “My name’s Aurelia, I work in your cochlea. Might I say it is very surprising to see you here?!” With that, she pressed into her own chest slightly, emitting a red glow somehow – and all of a sudden, the world around them changed. City Hall instantly appeared; towering and impressive buildings soared upwards; and hundreds of microponies appeared and stared in the direction of this unexpected encounter. Twilight couldn’t help but stare in awe at the inside of her own head – the architecture was sleek and modern, glass structures jutting out and swooping curves, high-tech transportation systems and screens - all giving the impression of an advanced and futuristic city. The sanitation was impeccable; everything looked clean and looked-after. It was amazing how many contrasts there were here to the run-down look of Rainbow Dash’s brain plaza. As some of the citizens gathered around her, the initial fear she felt - just as Rainbow had done - was soon washed away as she engaged in conversation with them: she was amazed to discover their impeccable intellect, for they were more than capable of maintaining sophisticated and academic discussions with her beyond merely behaving like a star-struck fandom. Aurelia even explained to her the camouflage spell, and the way to deactivate it across the city with the use of their chests.

Twilight thought aloud to herself, “I’ve been alive for years, studying all sorts of cultures and communities, and yet I never even knew that I was the host to a civilisation of my very own…” A few of her citizens laughed happily, and Twilight noticed the majority of these ponies were unicorns. “So, how does my magic work?”

A black stallion near the front spoke up with the answer: “Your horn gets its magic from the Magicians Institute built within it. Through receptacle tubes the spells are sent out to the horn which emits the spells out into the open – think of it as a downsized transmitter, and the Institute make up the ‘generator’!” A few other ponies cheered this, clearly members of the aforementioned department. Twilight simply beamed with pride and awe at all this, until the stallion noticed something.

“Wait a second…” he said, “I was just there at the Institute. Remember the Transvisceral Deposit, fellas?” A few of them nodded, but he explained to Twilight: “that’s the spell which transported Rainbow into her own head – boy did that take it out of us! Well, none of us knew or researched how to make that spell work for the self…we weren’t aware of an incentive effectively to cast the spell on our own Institute!” He turned away in his thoughts, “How could she do something without us knowing? Ah my head, I can’t even…aaah!” Almost driven to the point of insanity, he ran off to the amusement of his colleagues, but a few ponies were musing over his point too.

“I suppose I’d better go and see the Mayor,” Twilight pondered, and Aurelia offered to escort her. Again, City Hall was almost identical to that of the City of Rainbow Dash – the only differences being inside: sleek desks, high-tech equipment, futuristic interior design. Aurelia opened the door to the Mayor’s Office and said goodbye for now; Twilight thanked her and walked in slowly. The chair behind the desk had its back to her, as if the Mayor was looking out over their city through the surrounding glass windows. Twilight couldn’t help but feel a little bit unnerved to see television monitors showing her own head and body’s outline this time, with various lights flashing and indicating different things. The chair spun slowly and was revealed to be empty, but she heard a voice call out ‘surprise!’ to her, and suddenly the Mayor de-camouflaged himself sitting in the chair. He was a short unicorn, bespectacled and wearing a rather elaborate gown; his overall appearance resembling that of a wizard.

“Gotcha! Ah, Twilight it’s so good to see you – I never thought I’d get the chance!” He hugged her tight. “I’m Swirlestio, the Mayor of your wonderful city. It’s an honour to have you here.”

Twilight thanked him and they sat and had a civilised discussion about the city and its infrastructure, the small issue in Rainbow Dash, and the sources of magic here. Swirlestio revealed himself to be a masterful magician, skilled in all schools of magical thought. This was chiefly due to his life in politics - having had a father who was also a popular Mayor, and hence provided with premium exposure to the lessons from Celestia which Twilight was going through in her early years. When the question of the incredible camouflage came up, he explained: “Our camouflage spell was developed to disguise us from intruders, like a sort of spring-attack or method of ambush. Naturally, I’ll be happy to teach you the spell. You see, no city has ever been visited by one of our citizens; we are very ‘recluse’ since we have no reason to visit anywhere else when we live in scientific perfection! As a result, we have developed a special potion called “COGNITUM” for use on immigrants; it has the ability to extract unnatural essence and reveal organisms’ true forms – think of it as a highly-efficient border control! Last week we used it on some germs attempting to pass off as pathogens – I suppose the irony is that it could be used on our own camouflage spell!”

This gave Twilight an idea. “You guys must know the task I’m currently engaged with, then – curing Rainbow Dash, ridding her body of microscopic changelings?”

Swirlestio nodded, then lowered his head. “And we were not thinking straight with the Rainbow dream idea. Great shame. Let's share the blame...” he offered a slight smile.

Twilight was moved and also inspired by the sudden thoughts that crossed her mind, thoughts of mind and body working in tandem: my 'mind' is my own autonomous thinking, and 'body' is these microscopic helpers! Thinking back to Rainbow Dash, she spoke up. “I may be able to put it right, Mr Mayor. If you explain the camouflage spell to me, and give me the formula for Cognitum please, we can defeat those pests.” It felt very weird to her, basically negotiating and reminiscing with her own brain.

Swirlestio stood up and thought to himself, before eventually nodding in agreement. “You know what, Twilight? We thought we were the most advanced magicians around. However, your presence here has no doubt disrupted the space-time continuum and also defied the laws of physics – something which, quite frankly, only someone like you, Twilight, would ever do. Although most ponies’ bodies do incorporate a slightly independent subconscious from the City – that is, folks like Rainbow Dash have an inherent conscience not regulated by us – you have acted completely autonomously separate from us, from me and my teams…quite astonishing! We are all very proud of you.” He then pressed his intercom and sent for the Cognitum formula.

Twilight felt a tear of pride run down her cheek, assured and given a welcome boost by this. No matter what she did, she would always have this inner belief and support from a loving civilisation that was almost independent from her own thinking. It made her feel like nothing she ever did alone would truly be done ‘alone’; that she would never be alone as long as Swirlestio and his public were with her. Smiling, she realised she could now trust herself from inside, and, thanking Swirlestio, she readied her spell again. If I can learn to trust ‘myself’ from within, I must try to get Rainbow to learn to love and cooperate with her own internal community.

Rainbow Dash opened her eyes slowly, the weight of slumber lifted from her weary eyelids, but immediately she was given a startle as a massive tiki mask was staring her right in the face. “Aaah!” she cried out, until the mask bent down and Pinkie Pie revealed herself giggling. Rainbow sighed, “Pinkie Pie?! What the heck are you doing THAT for?”

Pinkie chuckled, “come on Dashie – laughter is the best medicine!” And she proceeded to distort her face through the glass of the beakers and tubes lying around the room, making silly noises and faces.

Rainbow did not seem amused. “It’s not helping, Pinkie...at least I can see again, thank Celestia! But my neck’s been itching all night, I must’ve caught a skin irritation from this silly blanket!” She rubbed her hoof on the back of her neck, and tossed the itchy blanket onto the floor. Pinkie bounced away into the hut’s main room, and Rainbow got up slowly. She looked in the mirror with weary eyes but was grateful to see that there was no shell-like texture to her skin nor fur, but her heart skipped a beat when she was sure her wings took on changeling form for a moment. She stared at them in the reflection, daring them to do it again until she was shaken out of it from the pink pony calling for her.

“Dashie! Breakfast time!”

Rainbow walked slowly into the room and found Fluttershy and Zecora around the cauldron. “Morning, Rainbow Dash – Zecora here has made an elixir for you to try, since Dr Horse's pills don't seem to have worked” Fluttershy said innocently, and Rainbow shot a disappointed glance at Pinkie for luring her in with the promise of breakfast.

Zecora walked up to Rainbow and said: “If your condition we are to heal, you must drink this elixir with unfailing zeal.” With that, she raised the small cup of green liquid and pryed Rainbow’s lips open. Rainbow muttered her complaints but was powerless as Fluttershy held her mouth open wide for Zecora, who presently poured the trickle of green into the cyan pegasus’ throat.

Rainbow swallowed hard and wiped her lips. “Eugh! There better be some waffles or something to get that taste outta my mouth.”

Back inside Rainbow’s brain, Twilight had undergone the same transition from her own mind back to where her statuesque physical form was befuddling her friends. Indeed Starlight, Spike and Discord all jumped when Twilight suddenly shook her head vigorously and groaned in discomfort. “Okay I’m back, sorry for leaving you like that…listen to me – I think I know how we can defeat the changelings here.”

“Wait Twilight” Starlight interrupted. “We just heard from City Hall that an unscheduled intake of liquid just reached the stomach – apparently it was some kind of medicine, do you think we should go check it out? Action Tremor had to leave by the way, he said he was sorry.”

“How do unauthorised things like that even happen?” Spike murmured.

Twilight heard this and snapped back the answer, “if you all let me finish, I’ll tell you everything Spike. The reason there’s a voicebox-override for the Mayor is because sometimes Rainbow Dash does things on her own. Like going rogue, okay?”

“Oooooh…” the foursome gasped together, and Discord raised an eyebrow of intrigue.

“Anyway, as I was saying. I know how we can get rid of the changelings. Yes, I visited my own brain – and yes, there’s probably a microscopic metropolis in all of us” – she was careful not to compromise the disguise of her own city – “and while I was in my brain, I was able to get the formula for a potion which will help us. It was stored in my brain, but I didn’t know about it – I literally didn’t know I had it in me!” She laughed as she proceeded to explain to them the Cognitum potion for which she now had the formula, and the camouflage spell which might be useful. They decided to rush to City Hall so Twilight could explain to Wellwisher her discovery, aware of the need to rush because Chrysalis could be anywhere by now - they had to get to City Hall before she did. The seven of them reached the plaza altogether, looking like a frenzied tourist group, and stormed into the building, bulldozing past a few lazy security guards and entering the Mayor’s Office. “Mayor Wellwisher!” Twilight bellowed from one end of the room, hurrying towards the desk as the Mayor’s chair turned around slowly, and Twilight locked eyes with the intense green ones staring at her.

“Yes Twilight?”

“I know how to defeat the changelings!” Catching her breath, Twilight steadied herself on the desk as the others did the same behind her.

“Well, how do I know you’re not a changeling in disguise? We’ve had hundreds of reports of mistaken citizen identity today…”

“I could say the same to you!” Twilight retorted, and so Wellwisher radioed her chief of police, who duly told her that Chrysalis had been sighted in Neck Hill, storming ponies’ houses and demolishing the neck's inside lining in the process. “Right. That’s cleared up, then...” Twilight proceeded to explain to the Mayor about the Cognitum and the camouflage potion, and Wellwisher pressed on her intercom.

“Get me the DAA Generals and the Science Deans from the University, immediately”. As the eight of them sat in tense silence, the door opened within about 10 minutes and four glum lab-coated ponies trudged in, accompanied by three military officials. Wellwisher described Twilight’s discovery and addressed the scientists first, showing up the Cognitum formula: “Listen up, this is the recipe for a potion which we are to administer across the city via the Respiratory air exhausts. We need to know who the changelings are, we need to be able to separate them. And you, officers – pay close attention to Princess Twilight. She has a spell for your soldiers to learn.” Twilight cleared her throat and showed the generals how to cast the camouflage spell. Two of them were unicorns and nodded in understanding; the scientists turned away with their formula – one of them even grumbled about ironically working for a giantess ‘city’ who consistently referred to their own profession as ‘eggheads’. Just as the gang smiled at the unfolding plan, one of the scientists burst back in quickly.

"Ma'am, there are some ingredients to this formula which we couldn't possibly obtain!" The blue stallion exhaled in panic as Wellwisher looked deflated.

"What are these ingredients?" She asked.

He re-read the list aloud. "Poison Oak, from the Everfree Forest; apple pips, and natural yeast." Wellwisher sighed at this, knowing the inhibitions of each: the forest was too dangerous for microscopic species such as themselves to venture into; apple pips always digested rapidly upon hitting the stomach acid; cultured yeast was hard to find and would probably be in the Canterlot labs. She sat back in her chair and rubbed her temples.

"Ugh this means we'll have to instruct the Wings, Muscles, the Vision teams, everybody! Nobody can work so intensely in these current conditions..." Just as she was about to reach for a phone, one of the scientists had a spasm and lunged for the Mayor, knocking the phone onto the floor and breaking it. The generals quickly detained the mad scientist, who revealed himself to be a changeling. He was dragged out of the office, laughing maniacally as if still in character. Wellwisher slunk back in her chair, a little shocked and even more at a loss now; with no means of direct communication to her teams in the various departments required, it was going to take forever to get the orders across!

It was at this moment that Starlight had an idea. "Twilight, I've got it!" Twilight turned to her sharply; as did Wellwisher. "You were saying how you knew Rainbow would be able to help us, right? This is the time to try again, to amend the earlier error of the dream, and get Rainbow on our side! I mean, she knows you and Discord are in here, so she'll be dying to know what's going on!"

The remaining scientists gasped, and Twilight's jaw dropped slowly as the validity of the idea sank in. "It's...perfect - if we can somehow get Rainbow to get the items herself, all we have to do is find a way to get them into her body for the scientists to use." She turned to Wellwisher, "is there some way in which I can speak to Rainbow Dash? Has that ever been done before?"

Wellwisher thought long and hard, "Hmm I don't think it's been done before, but I don't see why not - we have sound amplifiers in the ears; we can have them connected through to hear so if you speak loud enough into them, she might well hear you."

Twilight beamed, and sure enough the message was sent to the Hearing Dpt. to wire up the amplifiers. The team put on their earphones, turned the giant amplifiers to face the outer ear canal, and plugged in the cables that would send the input through to the microphone in the Mayor's office. She thought for a moment, and said to Spike: "Can you go down to the MSD and warn them to station some ponies in the throat, because we can't risk any of these ingredients getting disintegrated in the stomach? Tell them to make sure they catch the items as they pass down the throat." Spike nodded and headed off immediately. Licking her lips, Twilight switched the mic on and said softly: "Rainbow Dash?"

"Huh?" Rainbow Dash looked up from her comic, having finished breakfast and returned to a couch.

"It worked!" Twilight said excitedly to the others, forgetting the mic was still on.

Rainbow was even more puzzled, "Twilight...?"

"Yes! Rainbow, it's me, Twilight! Listen to me very carefully. I need you to- "

"Woah woah woah" Rainbow halted her, "where are you right now? Are you still in my head?"

"Of course I am - now listen, I'm afraid there's a rather nasty infestation in here and- "

"Now I remember...I dreamt about you last night, Twilight!" Rainbow interrupted again, and Twilight froze in fear at this as the others looked at her in horror. "Yeah, something about a prank, and a colon...but the important thing was I kicked some changeling butt, so thanks for that awesome dream!"

Twilight sighed. Okay, she hasn't remembered too much of it. Once more trying to speak, she began: "There's some annoyingly familiar organisms floating around in here, Rainbow Dash. I'm afraid if we don't do something soon, you could become a changeling yourself! No no, don't freak out - I know how to defeat them. We can do this together; you're gonna have to help me here. I've found Discord too."

Rainbow closed her eyes and breathed slowly, "okay, okay I can do this. I got this. We got this together, Twi. I'm not letting some changeling take over my mind!"

At this point Pinkie poked her head in to Rainbow's room: "who are you talking to, Dashie?"

Rainbow blushed, "Oh erm, no one...I guess this disease is making me more delirious....ooooh!" She faked a faint and laid dramatically down as Rarity might. Pinkie left with a shrug and Rainbow whispered now. "What do you need me to do, Twilight?"

Before replying, Twilight marvelled at Rainbow's independent responses to Pinkie. It has really developed now; Swirlestio was right - some ponies can be more autonomous from their inner-cities than others. She then replied to her friend: "We need you to get some stuff for us. The first is one of those blue flowers out near the hut - remember the one that nearly made you swallow Applejack?"

Rainbow Dash frowned, "yeah I remember it - and I'm getting pretty sick of having ponies inside me! But Twilight, won't those flowers curse me and my wings again?"

One of the generals shuddered behind Twilight, presumably scarred by the aforementioned events. She explained to her friend: "No it won't, because the magic the flower contains is being extracted for a different purpose. Don't worry about it. Now let's go!"

"Okay...here goes, I guess..." Rainbow opened the hut's door and walked into the forest, looking at her hooves on the ground until she - and indeed the ponies occupying her brain and watching RainbowVision - spotted the Poison Oak. "How do I...how do I give it to you?"

"Just swallow one."

"Ugh, fine!" Rainbow broke a sweat as she stood on the edge of the flowers, bending to pick one up with her mouth. Clenching it with her teeth, she tugged it out of its root and tossed it into her mouth. Inside the throat, Oovla watched as the giant blue flower came sliding down towards the uvula; she radioed her team, comprising about 30 ponies, stationed in the throat that it was incoming. The team eventually saw the huge flower surging down the throat, roaring its way slowly down with a 'gulp' from Rainbow. As it passed them, the MSD team fired industrial-strength grappling hooks into it, guiding it down to the stomach sphincter and carrying the large thing through and safely towards the harbour and populated area. The scientists were waiting there, and they flew up, extracting as much essence as they could from the giant blue petals that swayed around them. They finally gave the nod to the MSD team, who took the flower back to the lake of acid, and released the hooks - sending the now poison-free flower splashing into the acids. They radioed the Mayor's office to inform them of the first successful step.

"Nice work, Rainbow!" Twilight said encouragingly; she could hear numerous citizens outside cheering the same thing. "Now, can you see any apple trees nearby?"

Rainbow Dash looked around, leaving the forest now and heading into a field where, sure enough, a small orchard of apple trees grew. "Yes I can," she said smugly.

"Okay, just eat the apple."

"That's it?" Rainbow asked, but shrugged and ate the apple. When it was down to the core, she asked, "now what?"

"Discord and I need one of those pips. Think you can get one to us?"

Rainbow managed to extract a pip from the core, holding it up to her face - her massive eyes gazing down at the tiny thing in her hoof. "Yeah I guess I ca- aaah!" She stopped when she realised she had accidentally inhaled the pip into her nostril. "Aaaah get it out!" She tried to blow it back out her nose.

"No, don't!" Twilight urged, nodding to the scientists: the Nasal Passage might not have been expecting a giant brown zeppelin-like object to hurtle its way into the cavity, but it had lodged in the ground and so the scientists went off to extract what they needed. Again, when this was done, poor Rainbow was finally allowed to forcefully blow it out her nose - with the help of some tiny industrial jet-fans inside her nose. "Now the last thing we need is some yeast."

"Oh pfff easy, I'll just ask Pinkie for so-"

"No, Rainbow Dash - it's got to be natural yeast. That means it is undeveloped and the yeasts have not been- "

"Yawn, spare me the egghead lecture, Twilight - just tell me where I can get it... OW!"

"What happened?"

"I dunno, I just got a sharp pain in my leg...ow it really hurts..." Rainbow moaned, unaware that Chrysalis and some of her entourage had deliberately felled a musculatory column to make it harder for Rainbow to walk. Wellwisher intercommed for an Emergency Unit to be sent there immediately, accompanied by DAA and RDFD teams too.

"Don't worry, Rainbow - we'll take care of that. Now, do you think you can get to my castle lab?" She turned to the others and explained that she recalled she probably had some lying around in her lab; Spike nodded to confirm that she did. Rainbow Dash, meanwhile, gave a nod of compliance. "Great, let's go!"

As Rainbow was walking towards Ponyville, she asked: "So is it, like, totally weird in there, Twilight? What can you see?"

Eager not to affect her host's mentality, she tried to calmly dodge the question: "I can see exactly what you see, Rainbow Dash: we're nearly at the main street, and my castle's just off to the right." Rainbow walked into the castle, finding the lab under the occasional guidance of Twilight's directions. A tense few minutes ensued, as Rainbow was unable to locate the yeast, and Twilight couldn't remember where it was. "My log book!" She exclaimed, telling Rainbow to check the back pages for 'yeast' - and sure enough, they were able to find it on the shelf, a small jar of the yeast bacteria. "Now go ahead and swallow some of them."

"Eeew, I forgot yeast are tiny living things..." Rainbow moaned, put off the idea as she held the open jar. "I'm not sure I like the idea of loads of tiny thingies inside my stomach, Twi."

Several of the beachgoers in the stomach gave ironic cheers and laughed as this comment emitted from the RainbowVision screens, but Twilight pressed her friend on: "Come on Dashie, this is the last one and then we can kick these pests out once and for all."

"Okay, okay...here goes. Bottoms up!" Rainbow stuck her tongue out and wriggled some of the yeast out of the jar onto it. Inside her mouth, Oovla and co. watched as the enormous tongue slowly lurched back in, the closing jaws sealing the little yeast bacteria in their unexpected fate. With a gulp, they were lurched down the throat - only this time, the scientists had deployed giant nets to catch the yeasts in. The tiny yeast bacteria, round cylindrical fellas, writhed around and some even appeared sentient, shouting 'hey what's the big idea' and trying to squeeze through the net. An under-developed bacteria was picked up and the scientists' team extracted what they needed.

"Way to go, Rainbow! Now we can help the Mayor get rid of- ...I mean, now we may get rid of the germs here and have you back to your normal self! Go back to Fluttershy and rest with her for now." Twilight blushed at her slip, hoping it wouldn't cost her too much. She had been tempted to recall Rainbow back into her own brain, to try the dream once more - but only this time the entire area would adopt the camouflage spell with those red chests that Aurelia had told her about - until she decided it would have been too much of a risk and potentially damaging and undoing all their hard work so far.

"Thanks, Twi - I hope everything's okay in there...be careful with me, I'm too awesome to mess around with!" She allowed herself a cheeky chuckle, and Twilight simply shook her head with a smile. Silly pony she thought, and making sure to switch off the microphone the amplifiers through to the ears were cut. Wellwisher gave her a grateful hug, and some of the press down below congratulated Twilight on a superb 'broadcast' to the host.

20 minutes or so later, the scientists bulldozed through the crowd of media and press and hurried into the office, reporting that the Cognitum was ready and had been successfully tested. And so, the plan was set: there would be a citywide application of Cognitum, released into the Respiratory system pipes’ exhausts and thus emitting everywhere, separating the changelings from the citizens for good, and enabling the changelings to be overcome by the DAA, who were to be camouflaged to launch surprise attacks from numerous posts.

Chapter 5 - Working out a Workout

Later, citizens were enjoying an afternoon in the park, making the most they could of their city’s state. Having experienced sweltering heat the night before, they were happy to cool down in Upper Dermis Street Gardens along the interior of what was Rainbow’s left front leg. Here the temperature was being regulated after earlier vasoconstriction monitored by the S.w.e.a.t. Team – and with the weather now cooled, members of the public had braved the streets to relax. Similarly, beachgoers in the stomach had been greeted with pleasant conditions for surfing, with no food expected after an earlier intake of a syrupy waffle. In Neck Hill, repair crews had been sent to assess and restore property damage from the changeling assaults. Even the Optic Nerve thoroughfare had been restored to sufficient normality. All around the body, the citizens were doing their best to get on with their daily lives, ignoring the troublesome and growing changeling community among them. There was thus a surprisingly peaceful ambience. This all seemed in threat once again when the numerous pipes and tubes which swooped over their heads began seeping a gas through their vents. “Oh my god, it’s Chrysalis! She’s gonna kill us all with poison!” the citizens in the Gardens all shrieked, running for shelter and covering their mouths. (Poor Rainbow Dash, meanwhile, began to feel faint from all the veins' secretion of the potion around her body, and slumped in the sofa with a moan as Fluttershy sat with her).

However, the citizens’ suspicions were soon quelled when they saw some of the ponies fix in their tracks – as the substance crept around them, they appeared to crack like shells, in some discomfort: then a changeling was revealed underneath! As citizens and policeponies gasped, the changelings were left confused and looking around, exposed and uncovered. Almost as soon as this happened, a barrage of shouts came from a sweat gland nearby, and about 20 soldiers suddenly appeared, charging at the few changelings and covering their horns, cuffing them up and detaining them before they could do anything. The citizens cheered on their officials, confused by what had happened yet nonetheless delighted by the encouraging and speedy response to the gaseous emission. In the stomach, DAA troops had sprung up from under the pier to attack the exposed creatures, with the help of a multitude of locals. Neck Hill front yards were suddenly filled with soldiers, appearing from their camouflage and attacking the intruders on the streets. One particular unit were surprised to see one of their own soldiers break down into a changeling; they didn’t even hesitate to detain him. Several germs were also spotted across the body, their disguises as blood cells or pathogens and the like, being removed and revealing their illegal access into the city. All around the body, citizens and civil servants did their part in capturing the unwanted changelings. There were effectively two levels to the Cognitum now: the first layer revealed changelings in disguise, whereupon they were seized; the second layer of the potion would extract their changeling essence. Citizens whose identity had been stolen by a changeling presently returned back to their true cellular form once the changeling essence had been extracted by both the potion and forensic units of the RDPD; the changeling essence, bestowed by Chrysalis' earlier spell, was able to be contained and sealed.

Queen Chrysalis, who with an entourage had been nearing City Hall’s doors and was outside the Plaza at this point, was subdued by about one hundred soldiers positioned around the plaza, each one of them eager to be the one who placed that magic-nulling ring around her twisted horn. “What in Equestria is this madness?!” She yelled, struggling relentlessly as the DAA toppled onto her, her magic redundant. The five or six changelings with her were also snatched up before they could make a getaway, and again their changeling essence was extracted, revealing the poor microponies underneath, all confused. A flash of light whooshed over them and this prompted most of the soldiers to give way and allow Chrysalis to see – albeit tied down by various chains held by six soldiers each. Two enormous tanker trucks pulled up into the plaza; labelled Hazardous Chemicals - Keep Clear and Warning - Dangerous Specimens. The driver ponies got out and appeared to be readying their pipes at the rear. It was at this point that the floor nearby suddenly opened up like a hatch, and out popped Discord’s head. “Discord! What have you done, I demand to know?!”

“My my, you are hardly in a position to demand anything, Chrysalis” Discord replied smugly, as Twilight and Starlight burst out of the secret panel behind him.

“Enough, Chrysalis!” Twilight boomed, surprising herself with how commanding she sounded. “Your brief reign of terror is come to an end.”

Starlight smirked, “yeah like, I give you a 4/10 on the 'enslaving a community' scale…”

Twilight kept her gaze on Chrysalis, who squirmed slightly but tried not to show it, instead tugging at her chains in vain. Spike had returned from the MSD now, but Starlight and Discord moved so that they formed a triangle with Twilight around the changeling queen. “Ready Starlight? Ready Discord? Now, as we rehearsed…GO!” The three of them combined their magic as a great orb of yellow hovered over Chrysalis. The changeling suddenly felt herself being lifted off the ground and the soldiers duly let go of their hold on her; the orb clearly had her in its powerful grasp.

“Nooooooooooo!” In a flash, the big black creature was sucked into the orb’s centre along with her fading scream, and the tanker drivers opened up their pipe-valves. An almight roar of teal liquid came gushing out of the pipes, getting sucked straight up into the orb and following in after its creator. Indeed, every changeling's essence was slowly dragged into the orb, as if some sort of dystopian rapture were occurring. Microponies nearby watched in disbelief as the liquid jetted into this strange orb – which did not increase in size despite all the filling – and with one final surge and thrust from the three creators, it zapped itself into oblivion with a loud BEWP! Microponies emerged from their hiding places and clapped and cheered, not entirely sure what had happened but quick to surround the panting and exhausted Twilight.

“She zapped them to another dimension – they’re all gone!” Spike squeed to a neighbouring micropony.

Twilight added, “Remember the Pinkie clones, when Rainbow Dash helped me with the paint-drying test? We had to use a more powerful rendition of the same spell; Chrysalis and her changeling essences have gone to another dimension!” This was met by cheers of jubilation, and Wellwisher emerged from the ground hatch now, with two bodyguards, and hugged Twilight happily in front of the Rainbow Dash statue.

With their city rid of the infestation and being restored to relative normality once again from the various departments, citizens all around the group cheered in a chant: “Loyalty pays off! Loyalty pays off!”

Rainbow Dash sat and rubbed her head gently with a pensive frown, “hmm…changelings...d-dream...city?”

Fluttershy turned to her friend beside her, “Do you not feel any better, Rainbow Dash?”

“Actually, I do…” Rainbow said, “I mean, my head hurt a couple minutes ago but now I totally feel no pain at all!”

“Way to go, Dashie! Way to go Twilight!” Pinkie Pie cheered happily, erupting confetti from her spontaneously-appearing cannon. Hearing Twilight’s name made Rainbow smile slightly, as she thought of her selfless friend somewhere inside her body right now. Hopefully she knows too that she’s beaten it, whatever it was… Rainbow thought to herself, gently massaging her temples and stretching her limbs. With the three saying thanks to Zecora, they set off back for the town – and Rainbow even flew for the first time since getting her sight back, laughing with her friends.

Applejack bumped into them in Ponyville and noticed Rainbow’s recovered health. “Hey y’all – nice to see ya pumpin’ on all cylinders again, Rainbow Dash! Feel like hittin’ the gym later?”

Rainbow smiled broadly, “totally – I’m back to my awesome best now! Oh, but maybe I should wait for Twilight to come out."

Applejack raised an eyebrow, "Come outta where?"

Rainbow blushed, "oh er, nothing - just lemme go and freshen up at home first!”

The celebrations had continued throughout the city well into the afternoon, with all sense of time gone out the window. Every hub, every district, was filled with street parties, loud music and joyous festivities – even effigies of Chrysalis were being burnt in Lower East Side – and through RainbowVision monitors across the city, citizens watched happily as their host enjoyed the company of her friends without feeling pain of some sort! Twilight and her friends were on the beach inside Rainbow’s stomach, enjoying the beach party and sharing drinks at a poolside bar nearby. They even met Penelope Popliteal and Mary Pulmonary, happily restored back to normal and eager to spout their 'traumatising tales and experiences' to a rather bored Spike. This was suddenly interrupted when the RainbowVision screens blasted the sound of Rainbow Dash talking. "Twilight? Twilight! Come ooon, answer!" But Twilight was too busy out in the water, enjoying a fun stomach-acid snorkel and dive with some of her new friends. She saw various shipwrecks and food morsels, and even spotted the large half-digested flower sitting at the bottom of the belly. Just when Twilight resurfaced and paddled towards the shore, as several microponies were about to tell her what she'd missed, the screen belted out again: “Oh come on, again with this?!” All the startled microponies on the beach anxiously looked at the screen on the pierside hotel’s façade. Rainbow was looking in a mirror with her mouth open, and some of the citizens hugged each other and felt pride upon seeing their host’s face in the reflection. As the broadcasters zoomed in on the monitors, it was revealed that Rainbow had spotted graffiti on her uvula once again, right at the back of her throat.

Twilight emerged from the water and trudged up towards Discord with a growl, “go up and clean that right now!” Discord laughed innocently and headed towards the giant chute of the throat, chuckling at his own mischief.

Spike chuckled, “Oovla will be happy to see you again, no doubt…”

Over the course of the next 20 minutes or so, the group noticed various microponies wearing athletic gear, carrying gym equipment, going for jogs and such. The stomach’s lake of acid became a little bit sloshy and the beach was presently cleared; a nearby café’s TV reported news of Chesterton’s industrial productivity in the past 20 minutes, as locals busied themselves in their customary workout - and then the traffic update announced that the Circulatory transit system was experiencing no delays and a good trans-metropolitan service. “Rainbow Dash….is working out!” Starlight said excitedly.

She looked at the RainbowVision screen above them and saw an exercise bike in Rainbow’s line of vision, and sighed.

“What’s wrong, Starlight?” Spike asked.

“Well, I hope all these citizens get to party still and not worry about Rainbow hurting herself so soon after being ill.”

A familiar policepony walked past and offered a warm smile, “no ma’am, that is not a problem here. This city is just as awesome as she is; we’re always prepared for working out here – it happens often enough!”

Spike and Starlight laughed and trotted into the nearest gym on the boardwalk, joining in the fun on a treadmill as lots of other cells and microponies were busy exercising too. They even started a conversation with a filly micropony next to them, who chatted about life in the city as a youngster. Meanwhile, Twilight had met Action Tremor once more and the two strolled casually on the promenade when a klaxon sounded and a gush of liquid came pouring into the stomach acids, prompting a few ships on the horizon to unleash jubilant fireworks. The intake caused the waves to crash up against the shore – Twilight noticed the previously-corroded pier had since been rebuilt and bettered – and the smell of apples wafted into the two ponies’ nostrils. “Cider…” Action Tremor said, as Twilight rolled her eyes, noting a stain in the distance on the stomach wall, caused by excessive wearing from the acidic drink. They then listened in on the conversation as Applejack and Rainbow conversed between exercises, sweating and out of breath:

”So did ya hear about Trenderhoof?”

“No – you mean that show-off fashion guy Rarity and you fell out over?”

“Yup. He’s comin’ ta Ponyville again.”

“Oh…who cares?”

Rainbow Dash seemed uninterested, but her insides told a different story: the heartbeats increased, the adrenalin department were called to action and the Lust Team of the Emotions Department rushed past Twilight and Action Tremor whilst fixing their uniforms, having been enjoying a day off here at the beach. It seems some hormones had to be regulated. Inside the gym, Starlight and Spike cooled down and had also been watching the RainbowVision TV mounted on the wall. “Huh, who would’ve thought?” Starlight mused with a smile, as she and Spike reflected on the apparent crush Rainbow Dash kept secret. At this point, they saw Twilight walking past and they joined her, pointing at an amusement park further down the pier eagerly. With a sigh Twilight led them onwards as Spike bounced around happily.

“Looks like Rarity has even more competition for Trenderhoof’s attention!” Spike chuckled, as Starlight couldn’t hide her snicker too.

Twilight, however, looked pensive. “I dunno you guys, I feel bad for discovering poor Rainbow’s secrets like that…”

Starlight offered a hoof on her shoulder, “come on now, Twilight – don’t forget, we just saved Rainbow from a very threatening situation.” Twilight gave a reassuring smile, and the six of them presently arrived at the ‘Rainbowland’ amusement park – sure enough, the roller-coaster entitled ALL YOU CAN HURL was aptly named, as Starlight and Action Tremor both found their own stomachs couldn’t handle this ride within a stomach!

When the time came to leave, Mayor Wellwisher personally bid them farewell from the pier, with a whole load of citizens waving them off. An RDPD helicopter flew them up the throat after an authorised burp was summoned in the stomach. “Once again, I cannot thank you enough. What you have done for us, this city, and your friend Rainbow Dash – it cannot be expressed enough. You will always be welcome here and hopefully this city will stay safe for a long time yet! Who knows, maybe we will start to work in tandem with Rainbow herself from now on!” This was met by cheers and support from the public, and she hugged Twilight and waved goodbye. Meanwhile, the Breakdown team had created a bubble to slingshot them up to the mouth.

“Now remember our plan – once the bubble bursts outside, we’ll head straight back to the castle and we will re-apply the Zeromac’s counterpotion. Once we do that, there is to be absolutely no mentioning of what happened in here to anypony. Don't talk to Rainbow Dash about it - leave that with me. Okay?” They nodded, and they all disembarked the helicopter and penetrated the bubble as they rose slowly, thanking the pilot. As the burp came closer to the throat, they noticed the uvula above – and a snarling Discord in his hi-vis as he scrubbed his graffiti away, waving at them regretfully as they soared past towards the opening jaws of teeth. Discord tried to follow their bubble, but his ropes tangled and a laughing Oovla shook her head from behind the glass of her office within the uvula. She then told her assistant Toby to give the all-clear for the gaseous emission, and the mouth opened wide and the enormous tongue lowered slightly. With a massive BUUUUUUUUURP, the bubble was shot out of Rainbow’s mouth. Discord sighed to himself as he scrubbed his graffiti, wondering to himself: Why can I never resist?

Epilogue

Twilight raced towards the gym in town, she and her friends safely restored to their normal size, kissing the ground in gratitude. The counterpotion had been limited in supply and they had just had enough to apply to themselves. She spotted Rainbow Dash and Applejack wiping their brows as they walked out of the gym together; Rainbow was still holding a cider bottle. "Hey...guys!" Twilight found it difficult to address the pony whose insides she had just inhabited.

"Oh hey Twilight, where've y'all been today?" Applejack asked cheerily.

"Just sorting some stuff out in the castle, you know...I'm so happy to see Rainbow Dash back to her normal self." Twilight smiled and gestured silently to Rainbow to chat to her privately.

Rainbow turned to her fellow athletic friend: "Well Applejack, that was a good workout. I'll get back to my usual best soon, and then you'd better be worried haha". The pair exchanged muscle flexes and then Applejack trotted off. "Oh thank Celestia you're okay, Twi!" Rainbow hugged her friend and met her gaze. "So what happened in there?" She looked down at her own belly curiously as she sipped her cider.

"I'm afraid Chrysalis had managed to cause some trouble inside your body. Don't worry, it wasn't something you ate - anyway with Discord and Sta- with Discord's help I've sent her to another dimension." Twilight, breathing out heavily, prepared herself now: "I have to apologise though, Rainbow Dash. I may have cured your condition but I fear I may have hurt you unintentionally."

"Huh?"

"While I was inside your brain I was able to control a drea- "

"Twilight, who cares? I'm totally over it. Whatever you did, it worked - just please don't make me eat any flowers again." The pair laughed happily and began walking down the street. "So what was it like in there? It's all gross isn't it..."

"Actually, no...it's quite vibrant and full of life hehe...I guess my advice to you, to keep it that way, is to listen to your inner voice now and then." Twilight couldn't help smirking to herself as she thought of Mayor Wellwisher, not only hearing this now but also knowing it was referring to her.

"Okay, whatever you say!" After thanking her friend again, Rainbow parted ways with Twilight and flew up to her Cloudominium. As she flew, she looked around and took in the surroundings - but narrowly avoiding a bird yet feeling a sharp feeling in her right ear at one point - and she looked down on the small ponies below. Ah, everypony looks so small from up here...that's cos you're the best, Rainbow... "...wait a second." She sat on her doorstep and widened her eyes. "Small ponies...I'm the best... 'full of life'?! That dream...I should've let Twilight explain!" Panicky, she went to her room and had a shower, lost in her thoughts again as her mind wandered.

Princesses Celestia and Cadence flew into the enormous blue ear at speed. The hairs and earwax was everywhere, and Celestia seemed disgusted. “Why would Eevies even want to dwell in a place like this?” she asked rhetorically.

Cadence shook her head, “they may well surprise us. If your sister was telling the truth, it will be worth it anyway, to see this magnificent place inside young Rainbow.”

Celestia rolled her eyes, “yes, I know. She’s gone on about it enough.”

They followed Luna’s directions which led them down the canal, and after a series of twists and turns they arrived at the brain. To her horror, it was completely empty and there was no sign of a city anywhere; just a brain and cerebral matter, with electricity shooting out and little sign of civilisation. Cadence laughed, “oh dear – I guess your sister can’t control her own dreams!” After a sigh of disappointment, the two princesses headed back out the way they’d come. The citizens, meanwhile, sniggered as they removed their perfected camouflage spells amidst their laughter.

Author's Note

A huge thank you to OctaScratchRock, Voreafillyia and Tsitra360 for their creative input and help in making this story possible.

Chapter 1 - Hive Revive

Author's Note

A huge thank you to OctaScratchRock, Voreafillyia and Tsitra360 for their creative input and help in making this story possible.

Chapter 1 - Hive Revive

“Say aaahh”

“Aaaaahhh…”

“Hmmm” Doctor Horse took a step back from Rainbow Dash’s open mouth. Twilight sat nearby, glancing back and forth between the doctor and her friend with a worried expression.

“What is it, doc? Can you tell what’s wrong with her?” she asked nervously, twiddling her hooves.

“I’m afraid there’s no sign of irritation in the throat at all, Princess Twilight” Horse shrugged. “I’m sorry, all the symptoms you describe do not seem to be present at the moment.”

Rainbow closed her mouth, then spoke: “But doc, you’ve gotta believe us! I’ve had like the worst things all in one go!”

“I don’t doubt that, Rainbow Dash” the Doctor replied calmly, “flu one day, fever the next; headache one morning, poor hearing by evening…whatever you have contracted, my dear, it is not something I can offer a diagnosis on properly - at least at this moment in time, because it’s not something I’ve encountered before.” The two young mares looked dejected, so he offered more consolation: “What I’ll suggest is that we keep a close eye on you this week. For the time being, take these strong painkillers twice a day. Come back in a week or so.”

With that, the Doctor saw them off, and they headed back to Twilight’s Castle, where Rainbow had been staying recently whilst feeling unwell. As they walked through the streets, they tried taking their mind off Rainbow’s pain. “…and he acted as if he was actually with her as it happened!” Twilight laughed, recounting an earlier encounter with Quibble Pants.

As the two laughed, Rainbow sighed. “It’s gonna be nice to get into bed, I’ve been totally having a bad headache today….and the sore throat! Why does none of it show?”

“I don’t know just yet, but we’ll figure it out. Let’s get you to bed…” Twilight helped her friend to the castle lounge, and as Twilight left her friend on a sofa momentarily upon seeing Spike, the cyan-blue pegasus started winking at her randomly. “Um, Rainbow Dash, what are you doing?”

Rainbow struggled to control her own eyes, “great, now I’ve got random eye movements too?! Ugh!”

Twilight looked disturbed, “w-why are you doing that, Rainbow?”

“I can’t help it…maybe it’s a reaction to this stupid illness.”

THREE DAYS EARLIER

The City of Rainbow Dash was enjoying a vibrant, cheery afternoon. Citizens were in bright-spirits and the whole metropolis was filled with an upbeat mood. Rainbow Dash is such an active and vibrant pony herself on the outside that life inside her body was always going to be along similar lines. In the Downtown district, two affluent ponies – Penelope Popliteal and Mary Pulmonary - were having a catch-up in the beachside park, overlooking the lake of stomach acid as boats floated on the distant horizon.

“So yes, that’ll be in a couple weeks’ time” said Penelope.

“Well I really hope you enjoy it, I’ve heard Fluttershy is a fantastic relaxation getaway.”

“Indeed. I dare say life here hasn’t been too easy recently, and Mike can’t wait to retire. Circulatory transit management has just got too intense for him”. The two mares turned their attention to RainbowVision, proudly displayed on the large screen just outside the park.

“Oop, she’s found Gilda again…” Mary observed.

“Ah well, at least she’s having fun at the market. Gilda will hopefully keep sensible.”

At this point, the conversation on the outside was picked up by the screen as the citizens listened in:

“Come on, Dash, what’s the big deal?”

“Well...it fell on the floor, Gilda. In this puddle.”

“Why waste a nice cob?”

“Give me yours then.”

“No Dash, I wasn’t clumsy enough…chicken!”

“Oh, that’s it!”

A huge groan erupted from the audience as they all expressed their disappointment at their host giving in to the pressure. Sure enough, a klaxon warned citizens off the beach from the impending arrival.

“See what I mean?” Penelope urged. “Complete laziness. The new mayor’s trying hard but it’s simply not the same anymore for us.”

Mary nodded silently as a huge pile of chewn-up, yellow mush came splashing into the stomach, complete with full kernels of sweetcorn. “She loves that stuff, even if it’s covered in grime and illegal immigrants...” Mary thought aloud, and the two mares turned to the sound of breakdown units, border control teams and patrol boats setting off from the docks to conduct their respective duties, encircling the lump of mass as it slowly sank into the acidic waters.

Queen Chrysalis rose from the mess, shaking her mane of the salivary corn, and turning to the germs surrounding her. “That was indeed a fun ride, fellow troublemakers – and now to carry out my brilliant experiment.” A few of them seemed curious, but she remained coy and simply laughed at them. “Twilight and her ‘friendships’ may have ruined my hive - but this time I will surely get my revenge - now go! Spread your havoc as you informed me you would!” With a sinister laugh she watched as the various germs from the puddle licked their lips at the foolish pegasus’ decision to allow them entry; they jetted off in various directions and immediately confused the border control staff, but not as confusing as Chrysalis found these citizens' existence. “What in Equestria?” Chrysalis observed these microscopic ponies, coming onto the mound in their various teams, and noticed the unmistakable outline of buildings in the distance. Puzzled, she flew towards the shore rapidly – her appearance so bug-like that any passer-by would have suspected that dear Rainbow had merely swallowed a fly.

The queen stopped in the pier’s park and tried to hide inconspicuously behind a cellular tree. I can’t believe what I’m seeing she thought, completely captivated by the bizarre beauty of this unthinkable place, a fully-functional metropolis of microponies within somepony’s body. The swooping sides of the stomach rose up in the distance like evening skies, and the buildings were so intriguingly designed to fit this unseemly location. It was at this moment that she was spotted by someone.

“Hey, you there – are you spying on us?” Mary demanded to the figure behind the tree. Both she and her companion gasped as Queen Chrysalis slowly stepped out of the shadow.

“W-what are you doing here…?” Penelope asked nervously; startled as a fresh lump of chewed food splashed into the stomach in the distance.

Chrysalis looked upwards, inhaling into her nostrils the strange smells of almost-artificial landscape and sweetcorn. “Well,” she began, “ever since Twilight Sparkle and her friends successfully ruined everything in my latest attempt at revenge, I have been trying to revive my hive once again...now, from here I can execute a most spectacular punishment on that foolish alicorn and her friends! Mwahahaha!”

“But-“

“But nothing!" The two mares shuddered, gathering their things and turning away. “Not so fast!” Chrysalis called, and zapped them with her horn. The poor duo froze, engulfed in a purple haze which disappeared in a flash, dropping them to the floor and turning them into a pair of tiny changelings! “Success!” Chrysalis cheered, laughing evilly as the two changelings looked at each other and then faced their leader.

Chrysalis continued to dart around the park, zapping citizens and watching as they all transformed into newfound followers. A couple of strolling RDPD officers saw this eventually, but in trying to subdue the queen they were easily zapped too. Chrysalis glanced to survey her work: the changelings were scattered around the foliage and park, towered over by the skyscrapers of the harbour nearby, all looking at each other in slow understanding of their existence. Some of them were even sophisticated enough to adopt the micropony disguises they’d previously lived as. Excellent, now some of them can resume their jobs in this place - albeit terribly, mwahaha!. With a smirk, Chrysalis turned her attention to the pier and set off for it.

City Hall was a tense place. All afternoon, reports had been coming in of some sort of outbreak, an invasion of a species previously thought to be too large to infiltrate their borders – as a result, politicians and journalists were rushing about, TV crews setting up equipment everywhere, and reporters doing their best to catch vital snippets from the Mayor’s Office. City Hall were well-aware of the impending threat of the changeling queen causing havoc in their precious city. Indeed the Mayor, the cabinet ministers, city council and all the esteemed military personnel, had gathered to discuss the possibility of recruiting help from the outside world, namely Twilight Sparkle; their own defence forces were unable to overcome Chrysalis in their numbers due to her constant moving-around. Who better to vanquish the threat of Queen Chrysalis than the pony who’d done it so many times before? To get Twilight Sparkle’s attention, they had to send out an S.O.S – bear in mind that communication between cities was like seeking political protection – and so contacted the control centre in Rainbow Dash’s eyes, located in the remote Lens, to send out a hopeful Morse code message of winks to Twilight.