Shadow Generations: Harmonia in Chao
Aquatic Base
Previous ChapterShadow sat a bit awkwardly on a small pillow beside a café table. The pillow was soft even though it was drained of color, but he didn't think it was a comfortable way to sit in a public place. The ponies of this world must have thought it was since all the other tables at this café had them, but that wasn't the only thing making him feel awkward. He still couldn't believe this was actually happening.
Maria and Professor Gerald sat at his sides, and Thorax sat across from him. Thorax, per Gerald's request, was telling them about changelings, explaining what they were and how their magic worked. Shadow wasn't exactly paying attention, but he caught bits of it and noticed when Thorax demonstrated his shapeshifting magic to them, amazing Gerald and delighting Maria when there were suddenly two Shadows sitting at the table. He still didn't know what to do and he currently didn't have anything to focus on and distract him if even just for a little while.
He was brought out of his thoughts when he heard Maria ask, “Shadow?” He blinked and turned to look at her. She smiled seeing what she thought was a dazed look on his face and spoke softly to him, “Were you daydreaming again? You seem to do that a lot when we’re in class; it’s so fitting that you would do it when Thorax is trying to teach us about his species. It’s a good thing I’m always around to help you and keep you focused.”
Shadow blinked and thought about her words. “Classes aboard the ARK… That feels like another life entirely now,” he thought. He lowered his head, “And… you haven’t been here, Maria. Not for a long time… But maybe now…”
He raised his head and looked up, hearing Gerald ask Thorax, who was back to normal now, “So, your species feeds on… love?” Thorax nodded with an affirmative murmur. “I once read about creatures that did the same thing. Of course, that was well before I really began to focus on science and thus started to regard such things as myths, but it’s interesting to know such creatures do exist!” He raised an eyebrow, “You don’t… harm the ones you’re feeding off of when you do that… do you?”
Thorax quickly said, “No! No, no, I wouldn’t do that! I mean, I’m trying to see if I can sustain myself without having to follow the ways of my hive, and it seems like it worked earlier.” Seeing Gerald’s eyebrow still raised, he explained, “When I walked up behind you earlier, I could feel the love that Shadow and Maria have for each other. It was like it was hanging in the air and, like I said, I couldn’t help it; I just had to sample it. And, well… it’s been a long time since I’ve felt this full.” He turned to Shadow and Maria, “And you both feel okay, right? I mean, you don’t feel any different, do you?”
Maria replied, “Oh no, I feel fine! And that’s not something I can say every day.” At Thorax’s worried look, she explained, “You see, I have a… condition, and Grandfather has been doing research to find a cure for it.” Thorax nodded in understanding, so she continued, “I’m usually fine most days, but there are days where it gets so bad and… well, it’s hard to move around, or even be able to see, even on Space Colony ARK.”
Thorax tilted his head, “Space Colony ARK?”
Gerald looked at him and said, “That’s where I do my research, far away from prying eyes that might be planning to exploit it for their own ends. It’s also easier for me to monitor and manage Maria’s condition with her living up there.”
Thorax looked up and pointed with his hoof, “So, you live up… beyond the sky?”
Maria nodded, “Yes. You sound so surprised, Thorax. Is there nothing like that here in Equestria?”
Thorax looked down and answered, “Well, I’m not exactly from a place that knows about everything going on in Equestria, but no, not as far as I know.”
Maria looked up as she spoke, “There are a lot of things on Earth that I miss, but it’s nice living up in space too, among the stars. Even up there, they’re like diamonds. My Grandfather told me that it can take hundreds of years for the light of a star to reach Earth, and by the time we see it, the star might not even exist anymore.” She looked down at Thorax, “Isn’t that amazing?”
Thorax looked down at the table, “A light shines even though the star is gone…?”
Maria nodded, “That’s right.” She looked up again, “I wish I could see the stars here in Equestria. I wonder if they look different or the same.” She looked down and noticed Gerald had that look on his face that meant he was deep in thought. “Grandfather?” she asked, both Thorax and Shadow turning to look at him.
Gerald looked at Maria for a moment before he looked down at the table and mused, “I’m wondering about this temporal anomaly… What caused it? Is there a person behind all of this? If so, what are they like and why would they do such a thing? And just how far back or ahead in time were things pulled from?” He turned to Shadow, “You look the same, Shadow, but you’re quite different from the Shadow I know.”
Maria asked, “You mean like earlier, Grandfather?”
Gerald turned to her, “Not just that, Maria. There are other things…”
Shadow looked down at the table, suddenly unsure if this was the right time to tell them the truth. His thoughts turned to what Thorax had said. “A light shines even though the star is gone…” He was pulled out of his thoughts when he heard a crackling noise in his ear and realized it was his communicator. He glanced up at his ear for a moment before looking back down and saying, “Excuse me. I have a… call to take.” He stood up and walked away from the table, everyone staring after him curiously. When he was a fair distance away, he stopped and raised his right hand to his ear, saying, “Shadow here. Omega, is that you?”
On the other end, he heard the robot say, “AFFIRMATIVE. I HAVE MANAGED TO REESTABLISH RADIO COMMUNICATIONS THROUGH A WORKAROUND. I WAS ABLE TO TEST IT BY MAKING CONTACT WITH ROUGE. SHE REPORTS THAT SHE WAS ‘RESTORED’ BY SONIC AND IS CURRENTLY SCOUTING THE TOWN I MENTIONED EARLIER, WHICH IS APPARENTLY CALLED ‘PONYVILLE’.”
Shadow couldn’t help but feel a sense of relief at hearing that Rouge was okay, but he managed to keep it to himself as he replied, “Is that so? Good… that she’s not slacking off in the middle of a situation. Anything else?”
Omega replied, “YES. I AM STILL TRACKING THE OBJECT FROM EARLIER, BUT IN THE MEANTIME, ANOTHER TEMPORAL ANOMALY APPEARED MOMENTS AFTER MORE OF THIS CITY WAS RESTORED. IT IS LOCATED IN A PARK NOT FAR FROM YOUR CURRENT LOCATION. BASED ON MY SCANS OF THE AREA, IT WILL NOT BE HARD TO FIND THE PARK. IT IS COMPARABLE IN SIZE TO MERIDIAN PARK IN EMPIRE CITY.”
Shadow nodded, “Copy that. I’m on my way.” He switched off his communicator and turned to look back at the café table. At the moment, Maria was happily talking to Thorax and Professor Gerald was looking at them both, so it seemed like they were having a good time. He walked back over to the table and said, “I’m sorry, but… I have to go.”
Maria asked, “Go? Go where, Shadow?”
Shadow answered, “There’s still much of this world that still needs to be restored. And there’s someone I need to find. I have a new lead; I have to get back on the trail.”
Thorax spoke, “Well, we’ll come with you, then!”
Gerald turned to him and sharply said, “Out of the question! Maria was almost killed once already! I will not put her in any more dangerous situations if I can help it!”
Shadow nodded, “The Professor is right. I’ll be fine. We’ll all be fine. I’ll take care of everything.”
Thorax asked, “But, I can come with you, right Shadow?”
Shadow replied, “You’ve done more than enough already, Thorax. You should take the time to rest and recover, especially after earlier. Just find somewhere safe to hide first.” He turned and took a few steps before getting into a running stance and then taking off down the street with everyone looking after him, Gerald in particular having a concerned look on his face.
Shadow turned and ran up the side of one of the taller buildings around him to see if, based on what Omega had said, he could see the park he was looking for. A couple seconds of Boosting allowed him to get on the building’s square-shaped roof and he walked around as he looked across the city below. He soon saw it: a sizable area where there were no buildings, but there did appear to be small structures and trees and other plants rising up from the ground. He nodded; that had to be it. He leapt off the top of the building and started making his way towards it.
He reached the entrance to the park after a minute and he could see that it looked a bit dilapidated. Weeds were running rampant and as he started down the path in front of him, he saw a small stage for plays or music performances that looked to be in desperate need of maintenance off to his right. The benches in front of it were no better as they looked damaged and some of them looked like they had been thrown from their spots. “It looks like these horses… ponies are capable of leaving things abandoned as well,” he thought as he walked, correcting himself on the terminology used in this world.
After a few minutes of wandering around the park, he found the opening floating above the surface of a pond. He peered over the side of the arched stone bridge he was on; it was displaying the image of a circular room and a metal corridor on the other side of a doorway on its surface. “A base? One of the Doctor’s, perhaps?” he thought. Thinking of Eggman caused his thoughts to turn back to Professor Gerald and he paused for a moment. “The Professor doesn’t need to know about what his grandson does,” he decided before jumping over the side of the bridge and falling into the opening.

He dropped into the circular room he saw on the opening and he looked around. There were a few computer consoles along the sides of the rooms, but they didn’t look like they belonged to Dr. Eggman. He faced forward and looked down, bending down to take a closer look at the circular spot in the center of the room. There was a symbol of a bird-like creature with outstretched wings and what appeared to be the Sun above it etched into the floor.
Shadow stared at the symbol for a minute. Had he seen it before? “Maybe I saw it in G.U.N.’s databanks once. It doesn’t seem familiar,” he thought. He looked up at the corridor in front of him. Even if this wasn’t one of Eggman or G.U.N.’s bases, there was no telling what he might find further inside. He readied himself and then shot off into the corridor, turning slightly to follow the way it slanted.
Shadow passed through the doorway at the end of the hall and came to a stop. He stared for a few moments, taking in what he was seeing. The floor he was standing on came to an end a short distance ahead. There was some sort of metallic ball at the end of the floor and beyond that was a steep drop. There was no walkway over the gap, and there wasn't anything that he could jump to and run on to get across.
He walked over to the ball to examine it. Its surface was reflective and it was floating on its own. He raised his right foot and placed it on top of the ball. He saw the surface shimmer and the metal ‘splash’ as if he'd stepped into a puddle of water, but it felt firm to him. He stepped up on top of the ball and as he reached the center, it began to move. It didn't go too fast, and he quickly figured out that if he slowed his steps, the ball would slow down too. Somehow, it was attuned to his motions as well as the way he was facing.
“Is this some sort of experimental transport system?” he wondered as he maneuvered it around the corner ahead. As he turned to go around the next corner, he noticed a set of windows in the wall to his right and turned to look, raising an eyebrow at what he saw. “Fish swimming… This is an underwater base? Or maybe it's a laboratory, a black site even,” he thought as he kept walking.
It didn’t take him long to complete the crossing, slowing the ball down when he approached solid ground and jumping off when he was close enough. The door in front of him slid open when he landed and he walked through a short corridor into a much larger room. He looked up; there was a large column in the center of the room with a circular platform halfway up that looked it served as a way to reach the raised sections in the corners of the room. He faced forward and ran around the room in a circle. There were four doors on this level between the raised sections, including the one he just came through. The door to the left of where he’d come in from was open while the others were closed, so he decided to start there.
After a short hallway, Shadow found himself in a slightly larger room. He stopped and stared; many small metal spheres like the one he’d been walking on were floating around the room, and there was what appeared to be a pool of liquid metal on the floor with parts of the floor sticking up out of it in the middle of the room. There were also two cylindrical devices atop the metal ooze, one in front of him and the other at the other end of the room, next to a set of stairs that appeared to be damaged going up to another door. Curious, Shadow threw a Chaos Spear at the far cylinder. Upon being hit, the device spun and it begam to glow blue; immediately afterwards, the spheres in the room were drawn to it, crowding around it. “Interesting. Whoever this lab belongs to, their science is quite advanced,” he thought. He then moved to investigate the door at the top of the stairs, jumping off one of the spheres to get up to it.
Beyond the door was a longer corridor. As he ran, Shadow noticed two things: there were ashes scattered about on the floor and walls, and there was a strange black-purple streak going down the corridor. It was almost like a slime trail, but he had no idea what it was and certainly not what it belonged to. He decided he'd better not touch it as he kept running.
At the end of the corridor, he entered a room that had been either for testing or containment as there was a glass tube on a machine stretching from the floor to the ceiling in the center of the room. Said tube was broken with only a little bit of glass left on the bottom and top, but that wasn't the only thing in the room. There were windows going around the room that were all shattered, broken computer consoles lying along the edges of the room, and, worst of all, three bodies near the center of the room. They were all humans dressed head to toe in protective wear and none of them appeared to be moving.
Shadow stepped over the broken glass littering the room, making his way over to the nearest body. He knelt down next to it and checked; several moments later, he leaned back and shook his head. “Dead… And I'm sure the others are as well,” he thought. He stood up and walked over to the containment unit, staring at his reflection in the glass. “What happened here? What sort of experiments were they conducting?” he wondered.
As he was staring, he noticed a deliberate movement in the glass. There was something behind him, and it was creeping up on him. He remained still for a moment before whirling around and launching a Chaos Spear at it. As it reeled from the hit, he took a look at it. It looked like some kind of purple lizard with cracks along its body that were glowing. Its color made him think of the streak in the corridor. As he stared at it, five more suddenly leapt out of the floor around the center of the room. Shadow glanced in their direction for a moment before jumping up and throwing Chaos Spears at them as well, then turning to the first one and taking it out with a single Homing Attack. He proceeded to take out the others before they had a chance to recover and then ran out of the room.
As he ran down the corridor, more of the strange creatures appeared out of thin air. There were more of the lizards, but there were also smaller winged ones, and when he got back to the room with the metal spheres, there were also large worm-like creatures that came out of the floor as well as orange like lava versions of all of them. They surrounded the door leading back to the central area.
Shadow got ready to fight them, but then he noticed the cylindrical device in the middle of them and got an idea. He leapt off the first orange lizard that tried to pounce on him and twisted around to avoid the purple projectiles that two of the flying ones launched at him and threw a Chaos Spear at the device to activate it. As he suspected, it drew the creatures towards it, ripping their bodies apart in the process. He landed afterwards and looked around. “That worked, but what are these things, and what do they want? They seem too coordinated to be mindless beasts,” he thought. He ran back into the central area and found that the door on the other side had opened, so he ran through it, using more of the metal spheres floating around to reach the door on the other side of a gap.
The hallway beyond the door curved as it went down. It led to another short hallway; Shadow noticed there were spots where doors could close, no doubt in case of emergency. He found another large metal sphere in the room beyond, this one floating above a floor that was completely submerged under water. He didn't really want to know how deep it was, so he stepped on the sphere and started walking.
He didn't get far before he saw a white glow ahead of him, a robot appearing from it that hovered in midair. It looked a little like a G.U.N. Beetle, but it didn't have any markings on it to indicate it belonged to G.U.N. He heard a sound like it was loading a weapon; he didn't want to test how durable the sphere was, so he threw a Chaos Spear at it to knock it out of the air. As it fell, more appeared ahead of him, and they all turned their sights on him. He grit his teeth and started walking faster, trying to close the gap before they could fire at him.
He managed to knock out most of them, but one he overlooked fired its gun at him and one shot hit the sphere. The shot created a hole and the sphere began to compress quickly. Fortunately, he wasn’t far from a round platform, so he was able to jump to safety before he lost his footing. As he landed, a bunch more robots appeared suddenly, these ones looking more humanoid and coming in a variety of colors. Some were light gray, some were yellow, and some were red.
Shadow grunted, “Hmph! There’s no strength in numbers!” He then dashed towards them to prove it, weaving and dodging around their cannon shots and missiles as he fought back. It took less than a minute for the platform to be covered with scraps and pieces of wiring. Shadow knelt down next to one of the robots and examined it. “Is this one of the Doctor’s designs? It looks similar to his work, but I don’t remember him ever utilizing a design like this. The closest he’s done is the E-Series. And those other robots… Are they the same?” he wondered.

As he stood up, he heard a growling from behind him. He looked back over his shoulder; one of the purple lizard monsters from earlier was standing on one of the columns he had navigated around earlier looking at him. He just huffed and turned to leave; he didn’t have time for everything that had a problem with him. He had only taken a few steps when he heard a whirring sound followed a moment later by a cracking sound to his left, causing him to stop. He turned to look and his eyes widened; the creature was firing an orange beam from its mouth at the window across from it. It had been hit earlier by a stray missile from one of the robots and it hadn’t suffered any visible damage, but the beam was causing the glass to crack and it was sweeping it towards the other windows. “Oh no,” Shadow thought, realizing it was too late to stop it. He turned and ran towards the edge of the platform, using Chaos Control to teleport around to the other side of the room.
Back at the entrance to the room, Thorax flew in through the door and landed at the edge, looking down at the water below. He then looked up and saw the creature further ahead, still firing its laser at the glass. It had almost completed its sweep. Thorax wasn’t quite sure what was happening, but even from where he was, he was able to see when the water started to leak through the cracks, and his eyes widened as he realized what was about to happen. Before the glass completely shattered, he turned and flew back up the hallway, panicking more as he heard an alarm going off and the sound of water pouring in in the distance moments later.
He made it back to the circular room and flew up onto the raised circular platform in the middle, peering over the edge. It didn’t take long for the water to start pouring in and filling up the room. As he watched the water level begin to rise, he realized that the other doors in the room were closed, but this door and all the doors beyond it must still be open for the room to be filling up as quick as it was. “Why is that? Is it because of that Black Doom guy? Is he somewhere here too?” he wondered. He looked back down at the water; the room was more than half full now, but it seemed to be slowing down a little. He flew up towards the ceiling; he needed to make a decision. “I have to help Shadow!” he decided, readying his magic and steeling himself as much as he could as the water got closer.
Shadow, meanwhile, was skating as fast he could to stay ahead of the flooding. The alarm was going off and the red lights practically colored the entire hall he was running down. He entered another hallway and heard a computerized female voice say, “Area shutdown in progress.” He saw glass doors with the bird symbol in the center lowering down from the ceiling ahead of him and he shot forward, dropping down and sliding along the floor to make it under the last door before it closed. He stood up and continued running. He wasn’t sure the glass was going to stop the water, but he wasn’t going to stick around to find out.
More robots and strange creatures appeared to block his path as he ran. There were robots and monsters that were much bigger than any of the ones he’d faced so far, but he kept tearing through them as he kept going. That is, until he reached a room where there were windows on both sides. A shadowy figure that looked like a hedgehog appeared in front of each one and Shadow stopped in the middle of the room to turn around and look. They kind of looked like him, but their bodies were purple and seemed almost crystalline. They stared down at him for a moment before turning to the windows and unleashing a beam from their hands. It didn’t take long for the glass to crack, the water beginning to leak through.
Shadow turned and ran, trying to get out of the room before it started flooding in earnest, but the door at the end didn’t open when he approached it. He stared at it for a moment before turning to look back over his shoulder, the glass shattering and water pouring in a few seconds later. Shadow narrowed his eyes; getting out of the way of the rush of water was his best chance of getting out of this. He teleported up on top of the door frame and then teleported up near the top of one of the columns in the room holding the platforms up. He placed his hands on it and held on tight as he could, looking down at the water filling up below.
After a minute, the water had almost risen up to him and he was starting to lose his grip. He grunted as he tried to secure his grip and turned his head to look down again. The water was so close he could almost touch it. He wasn’t sure what to do next, but as he looked down at the water, he noticed something moving below the surface. He squinted, trying to get a better look at it. Suddenly, it broke through the surface of the water, revealing it was a black dolphin with light blue eyes. It took in a breath and looked up at Shadow. “Shadow! Quick, grab on!” it said in Thorax’s voice.
“Thorax?!” Shadow asked, surprised that the changeling had not only come after him but had managed to get this far in spite of the flooding. This wasn’t the time to wonder or say anything; whatever Thorax was thinking had to be better than staying put. He let go of the column and fell into the water next to the transformed changeling and put his right arm over his back.
“Take a deep breath and hold on tight!” Thorax said, both of them taking a deep breath before he dived under the water. He swam towards one of the broken windows and maneuvered around the shards of glass that remained. Once outside, he angled upward and started swimming as fast as he could towards the surface.
They could feel the water pressure pressing against them as Thorax swam up, the light above still distant. Shadow squeezed his eyes shut, trying to keep his mouth closed and avoid breathing in the water. As he focused, he felt something calling to him, feeling something shifting inside of him. Outside, Thorax saw several black trails beginning to swirl around the hedgehog, his desire to reach the surface keeping him going instead of stopping to stare. Tendrils reached out of the swirls, aiming for Shadow, though they stopped and retreated as Shadow opened his eyes and held his arms out, both of them suddenly shooting straight up towards the surface.

They broke through the surface of the water and fell back onto it after a moment, Shadow remaining on the surface on top of some strange creature while Thorax went under again for a moment. He then surfaced and stared at the creature in shock. It looked kind of like a manta ray, but it was made up of black tentacles like the ones that had been reaching for Shadow and it had a pair of red eyes on each side of its head behind its horns. Shadow raised his head and it shot forward as he balanced on its back, surfing on it.
As Thorax returned to his normal form and flew to catch up with him, Shadow looked around at where they had surfaced. They were surrounded by tall stone walls and towers, broken stone arches and pieces of walkways resting on the surface of the water. He maneuvered it around these obstacles and aimed for a flat stone square that had a set of stairs leading up attached to it. As he jumped out of the water, the creature disappeared, seemingly going back into his body as he landed on solid ground.
As he was staring down at his hands, Thorax flew up next to him and exclaimed, “Wow, Shadow! How did you do that? And what was that thing? Where did it go?”
Snapped back to reality, Shadow admitted, “I… don’t know.” He turned to the changeling, “I appreciate your help, but why did you come after me?”
Thorax stared at him for a moment before saying, “Well, you said to take the chance to rest and recover. I did, so I thought I’d follow you and see where you were going next! Maria and Gerald encouraged me to do it as well.” Shadow stared at him for a moment, then they both heard a light splash next to them followed by a ribbit. They both looked down; a frog was resting on the ground at their feet/hooves. Shadow looked to his left and saw a big, furry purple feline wearing a tan belt sitting on another stone square as he cast his fishing rod into the water. Shadow looked back down at the frog and bent down, picking it up. He then turned and walked up the stairs, Thorax following him even though he was confused.
The cat was pulling his line out of the water when he heard the footsteps coming down the stairs behind him. He stood up and turned to look, seeing Shadow walking down the stairs with Thorax following him. “Uh, hello. You’re Shadow, aren’t you? Hey, you found my good buddy, Froggy!” he said.
Shadow reached the bottom of the stairs and knelt down to set Froggy down, the amphibian hopping over to the cat. “He gets away from you a lot, Big,” Shadow remarked, though he sounded slightly amused as Big picked up the frog.
“Oh no. It’s more like a game, really. Froggy runs away because he knows I’ll always follow him,” Big replied. He looked up from the frog to Shadow and said, “We just got done with a game recently. Froggy got into the castle at Soleanna and I followed him. We even got to meet Princess Elise. She’s very nice.” He looked around, “We stepped into a glowing hole after we left the castle and ended up here. I think the old castle used to be here.”
Shadow looked down as he processed this information. “Soleanna… That’s why that symbol looked familiar. It’s the crest of Soleanna.” He turned to look towards the water, “But why would Soleanna have a hidden underwater laboratory hidden under their old castle? Was whatever happened there the reason the castle moved to its current location?”
While he was lost in thought, Thorax introduced himself to Big. “Hi! My name’s Thorax!” he said.
Big replied, “Hello. My name is Big, and this is Froggy.” Suddenly, there was a whooshing sound and everyone turned to see a hole floating over the water, displaying the Manehattan park on its surface. “Another one of those glowing holes,” Big remarked.
“It’ll take us back to the white world,” Shadow said. He looked at Big, “Come with us. You can find more places to fish in that park and the city.” That seemed to pique the cat’s curiosity and he followed them into the hole, which closed after they were all through.
Shortly after they landed back in the park, near the pond with the portal Shadow and Thorax had gone through, the park regained its color along with the street outside of the park’s walls. Big looked around while Froggy rested on the palm of his left hand. Thorax looked at him and said, “Equestria doesn’t normally look like this. There’s usually a lot more color and noise.”
Big replied, “Oh, I don’t mind. I like the silence.” He turned and walked over to the nearby pond, “It’s easier to focus on the fish.” He sat down at the edge of the pond, casting his line into the water. Both Shadow and Thorax stared at him, each with a bit of amusement on their faces.
Unbeknownst to any of them, they were being watched, not by Black Doom, but by another being, the one who caused the flooding of the lab. It was unable to do anything itself at the moment as it was currently sealed away, but the temporal anomaly was weakening its prison, allowing its power to spill out. Its green and pink eyes focused on Shadow, burning with hatred and desperation. Desperation for freedom. Desperation for its desire to exist.
Author's Note
Hooray, another chapter out! I hope it's to your liking. It's currently a bit late at the time of posting.
What's there to say... Well, the part about with the flooding was inspired by the Sonic '06 level pack for the fangame "Sonic Robo Blast 2" by Mikhael Blur. The Aquatic Base level features several areas that are underwater.
A lot of the dialogue is pulled from the optional conversations in the game. Aside from that, I can't think of much else that needs elaborating on. Let me know if I'm wrong. Until next time!
