The following Sonic story, other rather, Eggman's, is set after Sonic Generations.

An Empire's New Beginning

"Yes, Maria. Under my rule, the world will be a better place. However, that blue hedgehog. He's an obstacle that always gets in my way! There has to be a way. To have the world under my control, that rodent and his disgusting friends must be removed. Is it possible to rule the world and destroy that fiend at the same time? No. Even if that hedgehog's gone, there are others trying to oppose me. G.U.N., countries' militaries, Shadow, and other potential rivals. There has to be an alternative way. To rule this world and eliminate that hedgehog. There has to be another way. Another way…Arrggh…But how?! Where…am I going to…where…am I?" His vision whitens before it darkens. After that, everything became clear.

"A promise. I made a promise, Maria?" Doctor Eggman wondered. "Was it a dream…or was it a reminiscent of the past?" he asked himself. He was slowly getting up from a chair. "Strange. I wasn't seated the last time I slept. Where exactly am I?" He looked around with his vision recovering from where he had slept and a familiar scent was returning to him. He understands now where he's at. The control panels, a jungle view in the window front, computers at his command, a robot maid making the room clean as ever, and a master chair to boot. He's in the Captain's Room of his mighty Egg Carrier stationed within the jungles of the Mystic Ruins.

"Good morning sir." asked the robot maid. "Is there anything that needs to be done?"

"Huh?" a little bit surprised before going back to his usual behavior when at his command ship. "Oh..umm…ahem…This isn't much for you to do here. You can go on ahead, take your leave, and scram." He swipes his hand to shoo it away.

"Very good sir." and with that the robot maid left.

"Now where was I? Oh yes, how did I get here? Last time I remembered, I tried to defeat Sonic with my other self using the Time Eater by destroying the fabric of space and time. Was everything that has happened a dream?" He contemplates his memory while scratching his chin. "Computer!" he commanded with the monitor appearing in front of him. "Show me the status of Eggman's Incredible Interstellar Amusement Park." The computer showed him where his amusement park would be at, at least the remains of it with the elevator tower still standing. However it is being torn apart by government forces.

"What the," the egg-shaped doctor zooms in closely at the elevator tower that once held his galactic amusement park. It's being torn apart by G.U.N. agents in their vehicles, ships, and mechs. The mechs were dismantling the elevator piece-by-piece and the vehicles shipped them back to Earth as salvage. "Those G.U.N. geeks are destroying what was left of my amusement park! Curse them! And I was just planning to use those parts for recycle to rebuild bases of my empire. Damn them all!" He stomps the floor two times before calming down to think logically. "They won't find anything from there. All the files I've had at my Incredible Interstellar Amusement Park were destroyed. This also confirms my theory that using the Time Eater against the hedgehog was not a dream." He then remembered something that his genius brain apparently neglected.

"Wait. Then what about Cubot and Orbot?" he ask the computer. The screen enlarges to zoom in parts of space where his two robot assistants would be at. The yellow, cube-shaped robot was seen scratching his head before moving excitedly around a red orb-shaped robot, who appears to be lying down as an act of boredom and annoyance. "Hmph. Figures. That's what Orbot gets for trying to find that voice chip." Even though the doctor was the one the ordered the voice chip to be fixed in the first place. The two robots stopped at what they're doing and began swimming towards a nearby rescue ship. To Eggman's dismay, the rescue ship was a G.U.N. ship. "Oh no. They're going to be captured! If they're going to be captured, they will reveal my secret bases around the planet, even the Egg Carrier! Activate self-destruct program on Cubot and Orbot!"

"Request has been denied," the computer responded. "Action cannot be performed as units Cubot and Orbot have no such program within their functions and design."

"Ugh, this isn't good. Why didn't I plant the bombs in those idiots? Oh right, it's because they are idiots. But they hold key information of bases planted around the world!" By now the doctor would've panicked and fearing for his life right now if the computer hadn't slammed at his face to get his attention on further development. "Oh what is it now?! I can see that they're being captured, interrogated, hacked for information and…wait." He looks closely at the screen. Before his two robots enter the G.U.N. ship, it released a space pod from its rear. After Cubot and Orbot boarded ship, the G.U.N. vehicle took aim at the pod and fired missiles at it. "What are they doing?" Eggman could see that afterwards the ship flew towards the elevator, shooting down mechs and vehicles salvaging the pieces, and was last seen fleeing back to Earth. "What on earth is going on? Computer, when did this happen?" he demanded.

The computer answered, "29 minutes and 55 seconds. Still counting."

"About half an hour. Then that means…" He checked the security camera stationed at the entrance of the Egg Carrier. The camera shows that the same G.U.N. ship is parked outside.

"Master, you have visitors," a robot maid said through an intercom.

"Oh no. This isn't going to end well." He turns around to brace himself on whatever surprises may happen. The automatic door opens with something he least expected.

"Ta-da!" confetti were tossed in the air.

"What the -!"

"Surprised you huh doc! Did I surprise you? Of course I did!" the yellow cube-shaped robot was talking in a giddy girl's voice who likes to throw parties. "I was like 'Ta-da!' and you were all 'What the-!'" emoting everything that's happened.

"Cubot!" Eggman pushed him aside. "What are you doing here? And what's going on?" questioned the mad scientist.

"It's good to see you again too boss," said the red orb-shaped robot in an exciting yet sarcastic tone while following behind Cubot.

"Orbot, care to explain what's going on?"

"Well you see here, we've been rescued from the distant parts of space. Now it's good to be back to a place where anywhere can be home, on aboard the Egg Carrier." Apparently that was supposed to be recited when referring to the battleship that can fly around and be stationed anywhere. It gets pretty bothersome when used repetitively. Even the doctor's getting annoyed by the redundancy.

"Yes, I can see that." Eggman points to a screen showing the video camera of a vehicle parked outside. "And who exactly brought you back here?" An automatic door can be heard faintly as it opens with footsteps following along.

"Ah yes. We have been sent here by a kind, yet rude gentleman who is ummm-"

"Standing right behind you." A middle aged, male voice was heard.

"Oh, umm. Wha!" Orbot turns around in surprise. "I'd say! How rude! You can at least try to make a good impression in front of the doctor!" He demanded the pale-skinned man dressed in a lab coat, with white hair, and dons horned-rimmed glasses. The man pushed back his glasses with his middle finger in response to Orbot's outburst.

"So it was you. You were the one who brought back my robots." Eggman said to the stranger.

"Indeed I have. Allow me to introduce myself. I was codenamed WMD, top leading scientist for G.U.N.'s weapons, technology, and research development. You may call me Dr. Mod, or just Mod for short." He takes a bow and gives out a handshake. "At your service."

"Yes." Eggman said in a formally polite, yet still holding suspicion. "The pleasure's all mine." He shook hands. "So what you brings you here, G.U.N. scientist?

"I was a G.U.N. scientist," He reminded the past tense. "Now that I quit by force as a shift of alignment to you."

"Really? Care to elaborate what you mean by 'force'?

"It's a top secret procedure for G.U.N. scientists to be bonded to G.U.N. for a lifetime, even under retirement. They didn't want any top secret files, projects, and intelligence regarding weapons of mass destruction leaked to the public, so they would have our contracts terminated if we were to leave, publish our research notes, or leak out sensitive information in our daily lives. Fortunately, I was able to express my resignation with my neck intact."

"Risking your life to come to me. Yes, I may have some use of you, but what do you expect in return?" Eggman thought in his head.

"And I'm sure you've seen it," pointing to a screen showing the earth's atmosphere. He walks towards it and rewinds until the part of his transgression showed. "Originally the mission was to find any valuable data to exploit your means of world domination. Around where your supposed theme park would be at, we found nothing. So we just pick up whatever's left like materials used to build the elevator. Then we saw two active entities going on about in space. A rescue team was formed, and we found out that they happened to be those two," pointing the two robots in the Captain's Room. "The mission was to extract data from them to pinpoint your bases and exploit them. But I have my own objectives..." He made a grimaced smile while pushing back his glasses. "Agent Steve and his annoying bunch. They've been a thorn on my side for a while. And to think they actually believed they have to use a space pod to retrieve those machines," snickering to himself while referring to the two robots. Cubot was angered by that comment. Orbot had to hold him down.

"He just said we're machines!" Cubot whispered in his normal yet obnoxious voice.

"I know it's rude, but that's because we are. Let him finish his part of the story before we can have a say in it."

Mod continued on, "And shot them right on. Bam." He said with the video replaying his missiles hitting his target as done in the past. "After that I had to destroy any witnesses and evidence before the Central Information Agency can blacklist me. While I was on my way to Earth, I had to hack into your robots to pinpoint your base location."

From that, Orbot begin to step in. "That was very rude of you."

"Yeah, haven't ya heard of mindin yer own business!" Cubot said in a Sicilian, mafia accent.

"You've even broke Cubot's voicechip. After we've worked so hard on fixing it." Orbot lamented.

"And yer could've just asked!"

"I did. You just said the doctor found a purple energy source with eyes and a mouth and he simply disappeared."

"We were telling the truth!"

"Yes, but unreliable ones. I need to know specifically where he's at. I assume he should be at a base mobile enough to be anywhere. And here he is."

"Yes," the Doctor confirmed. Mentally to himself, "Though I don't even know how I got back here in the first place. Moments ago I was lying on the floor of limbo with my past self. I slept and when I awoke I was back at the Egg Carrier. I'm going to have to contemplate on that later. For now I have to test this new accomplice." Eggman begins to ask the questions. "So why did you come here? What purpose do you have in service of me?"

"The Commander-in-Chief has made proposals on cutting down G.U.N.'s weaponry, including the ones in development. If that were to pass, they wouldn't have any need for scientists who developed them, and of course I had already explained what happened to those whom G.U.N. wouldn't have any use for in the field of secrecy.

"So you've defected G.U.N. and join me to save your life?"

"Oh no, it's not just that. It's actually a lot simpler. I like to see the results of my weapon projects go through and made its use. To the president, there was no need for more weapons as there are no wars concerning the United Federation. Most of the conflicts they had were with you and all they had to do was stand idly by while a blue hedgehog does their job for them. I enjoy doing something, and I couldn't stay in G.U.N. any longer if they aren't going to give me any orders to do so. I could at least do it with someone that does."

"Hmm. Not a bad idea on your part, and I always enjoy telling people what to do other than robots. You're hired."

The former G.U.N. scientist smiled, earning the envy from Cubot and Orbot. They would have dwell on that feeling if they weren't listening any further of what the new recruit had to say, "There was a vacant space while I was on my way to the Captain's Room. May I use that as my research facility?"

"I don't really have much use for that room, so you may do as you please."

"Splendid! My assistant is already setting it up."

"Your assistant?"

"Yes. He should be here soon," Mod looked at his watch. "So what's next on the agenda?" he asked his new employer.

"I've been thinking," Eggman answered. "Whenever I try to take over the world, Sonic and his friends are always there to stop me. And when I try to build something or come up with a strategy to destroy that meddlesome hedgehog, there's always a third party interfering. It seems that no matter what I do here on earth, I never succeed. Back in my visits to alien planets however, no one's been able to stop me. No Sonic. No G.U.N. No one."

"So what you're saying here is?"

"In order to build the Eggman Empire on Earth, I have to build my army and formulate my plans elsewhere. Once I gain enough strength and firepower, I'll be able to take on Sonic, G.U.N, and… the world! All I need right now is a Chaos Emerald to power my Egg Carrier and reach a different destination."

"And where would that be, doctor?" Orbot stepped in to ask.

"Anywhere. Far away from here. It could be in another planet. It could be in a different dimension. All I need is one Chaos Emerald to induce Chaos Control for travel. And I can't have that hedgehog and his friends involved lest they may foil my plans."

"Now where would we get one?" Cubot asked, this time in a more thuggish voice.

"You guys are in luck then." Mod pulls out a green piece of jewelry out of his lab coat. "I happen to have one already."

"A Chaos Emerald?! How did you get it?"

"G.U.N. always has a spare just in case. And as their top scientist, I was eager to do some research on it. Of course, it wasn't easy getting my hands on it, especially when a certain agent wasn't willing to lend it."

"Indeed. Cubot! Orbot!" Eggman ordered.

"Yes sir!" They both said in salute."

"Prepare the Egg Carrier. We're getting off this planet." The yellow and red robot moved in forward to the control panels, setting coordinates, and the Egg Carrier lifts off. "So the agent?" Eggman asks Mod, knowing that the upset agent likely Shadow. "He's not going to suspect it?"

"He probably thinks I'm dead. Which reminds me." Mod pulls out a remote detonator and pressed the button. The G.U.N. ship that was parked outside before the Egg Carrier took flight exploded. "I had to make sure there's no evidence left behind before we make our journey."

"Crafty and resourceful. You'll make a fine addition to the Eggman Empire," the doctor complimented to which Mod thanked. "And without further ado," Eggman pressed a button, activating a beacon to appear from the floor and placed the Emerald on the beacon after seating on his master chair. "Activate Chaos Control, now!" Unbeknownst to him, a hum of an automatic door was made. Upon opening, the entrance reveals a dark figure walking towards Mod, who's standing beside Eggman.

"Did I miss anything?" said the dark figure.

"No, my assistant." said Mod, the former GUN scientist. "You're just in time for the phenomenon." Eggman was about to look at what this assistant looks like, but he shrugged it off for later as he's focusing right now on the Chaos Emerald. With the Emerald's energy channeling through the beacon, the ship's power enveloped in a green flow before everything around began to disappear from earth. Everyone in the ship had their eyes shut from the flash.

There were no witnesses to everything has that happened so far in the Mystic Ruins. The exceptions are two, a cat and a frog.

"What was that noise, Froggy?" asked Big in his usual slow voice.

"Ribbit," the little frog jumped.

"That was the Egg Carrier we just saw," stating the obvious. He looked out further from the jungles and saw an explosion after the Egg Carrier took off. Then Big looked up at the battleship and saw it disappear in a green flash.

"That Eggman must be up to something, and it's not good."

"Ribbit," groaned Froggy.

Meanwhile in the flying fortress, everyone had opened their eyes.

"Orbot, what's the status situation?" Eggman asked.

"Well, it seems from our teleportation we're not on earth," The robot replied.

"I know that! That wasn't a rhetorical question," retorted the doctor.

"Oh, um, yes. It is nighttime. The moon is really bright. And from what I've gathered, there is an overcast of clouds below us. The weather scans indicate that it's currently raining, but we're not getting any showers here."

"That's because we're above them you nincombot!" Eggman throws a wrench at the red robot.

"Oh dear." Unlike his yellow partner who would take the hit, the orbed-shaped automaton folded his arms and head into his body. His round shape structure deflected the blow from the wretch and rolls slowly back to his original position. "Oh what did I do to deserve this," Orbot moaned.

"And that's not aww doc, it wooks wike we got owselves company." Cubot stated in a voice of a hunter for rabbit season. The captain and the crew looked closely through the windows on the outside. They could see around their massive airship a flock of equines flying on the clouds and in the air.

"Oh my, horses are flying in the night sky," his red partner replied.

"They wooked wike ponies Owbot."

"Owlbot!" he misheard. "I swear we really need to fix that voice chip of yours."

"They have wings on top of them," a dark, creeping voice from the assistant replied. "They must be pegasus, pegasi for plural."

Cubot and Orbot were chatting around about the voice chip and the perpetrator who caused it. When they turn around at the horned-rimmed subject of their conversation, they could see that same person standing next to their creator had his accomplice brought along. The being had the looks of a black creature with similar appearances present behind the doctor's back.

"Hey Doc, doesn't he -" Cubot's comment came to stop when Orbot grab hold of his partner.

"Shh. Remember what Mod said?" They looked at the man in the white, lab coat with a 'shush' gesture along with another saying 'not yet'. "He'll have our nuts and bolts if we introduce too soon."

"Yikes." Both robots turn back around in their positions to pilot the airship while avoiding suspicion of the bald doctor. When they return to their post, a pegasus in gray coating, blonde hair, and crossed eyes was slammed flat in front of the cockpit. This surprised the crew, seeing one of creatures up close. They could barely, but can hear what it had to say.

"Sorry. My bad." It slipped to the side as the ship went through a cloud decorated with rainbows.

"That was an odd turn of events." Orbot bluntly stated.

"I know. I mean was that a mawe ow femawe"

"You mean male or female? And that wasn't my concern. It looks like that cloud was very ornate. If we went through it, oh dear, it'll be our responsibility for ruining someone's work of art."

"Those things are all too trivial!" Eggman shouted, earning the stares from the crew. He then calms down from his outburst and recovering from all the sudden changes like the pegasus and the rainbow cloud. "No matter. Trivial as they may be. They provide insight on where we're on and what we're going to do next."

"Indeed." Mod bowed in reply. "What's our next course of action?" Eggman remained silent. After going through a cloud colored with rainbows, the Egg Carrier was traveling over a large dense of forest. Upon reaching the edge of the forest, they could see a large gap between the edge and the other side, a fog down below the canyon, a fragile bridge connecting the two sides, and a ruined castle structure where the bridge leads up to. The computer scans showed physical parts down in the ravine, so they weren't too blinded from the fog when descending in the gap. Finally Eggman answered Mod's question.

"We'll need to establish a base here and build up fortification. Once we have that, we'll need to gather intelligence of our surrounding area and this world. Then, we'll know what to do for our next course of action. The ravine is a start for my settlement and fog above provides cover. The castle over there is something I have my eye on. Now then," he turns to his robots. "Cubot, Orbot. Off to the assembly lines. We'll need some Egg Pawns on the double."

"What do we need the Egg Pawns for, doc?" Cubot asked.

"To start building our base you nincombot!" He kicked Cubot to a wall, who then later bounced off and did his performance trick like the last time he was kicked.

"Ta-da!"

"Grrr." Frustrated, he shouts, "Get to work already!" And with that, the robots fled. Mod stepped in forward to pick the green gem from the beacon.

"In the meantime, I'll be working on the Chaos Emerald. I've been wanting to do some research with it."

"No. I will need you here for armament. We need to manufacture troops in case of an emergency."

"Very well then. I will leave my research here with my assistant." He walks down behind Eggman to give the gem to his assistant. Eggman wanted to see what he looked like after finding space for his base, so he turned around and was shocked to see what the assistant looked like.

"S-Shadow!" He could see before him the Ultimate Lifeform. However, he was different from what his grandfather created. Unlike the black hedgehog whom he knew had the color red on spikes, shoes, and eyes; the one he sees before him had gray spikes, green eyes, and no mouth.

"This is not Agent Shadow. Please introduce yourself." The former G.U.N. scientist commanded his assistant before he could take his leave with the Chaos Emerald.

"I am Mephiles. And as I am to Mod," he bows, "I am at your service." He gives out a handshake.

Mephiles. Where have I heard that name from? Ignoring his feeling of Déjà vu, the doctor shook hands with another new recruit and replied, "Yes. Well, you know what they say, the more the merrier."

At first you may think that the black and white figure were Rouge and Shadow from the previous chapter. Nope, it turns out to be Mod, a human OC, and Mephiles.

After the events of Generations, Eggman finds himself in the Egg Carrier. To confirm whether or not everything that has happened a dream, he looked at past events in Colors. And while thinking about the past, he looked to the present with his apprentices' arrival along with some new ones.

Since his attempts at world domination sucked at earth, maybe he'll find some success in other worlds before going into his own.

The Ancient Castle of the Royal Pony Sisters may face some remodeling. Based on the second episode of the first season after the expression of Loyalty.

Who is Mod? Just an OC I just made up for convenience. No one really important. And Mephiles? How did he came to be after what's happened in Sonic 06. It's almost the worst game in my opinion since I kept on dying due to inconveniences though the boss fights were very enjoyable. Sonic R was the worst since I can't get the controls right or even win 1st place in a race with little to no cars in it. Back to the topic of Mephiles, whatever theories you've come up with I appreciate it, but everything will be explained in later chapters.

Shhh. Be vewy vewy quiet. I'm hunting ponies. Wait a minute. The tagline was supposed to be SA2's Dark Side trailer. Ahem.

Long Live the Eggman Empire

Sonic the hedgehog characters, settings, and related materials are © to SEGA. Created by Yuji Naka.
My Little Pony characters, settings, and related materials are © to Hasbro. Created by Lauren Faust for television.