The remains of the pony in the glass-like tube were nearly still, moving only as occasional aeration bubbles passed through the viscous fluid. The figure itself was narrow and thin, its face sunken and corpselike. Even its wings were so thin that Thebe could see the blood pumping through their vasculature.

No pony in Equestria would have recognized this creature, though. Even if it had been complete- -if all the limbs had been attached, or the torso were the proper size and filled with organs, it would look unlike anything they had ever seen. Its tiny eyes, extended face, or the strange gate it would have had when it walked with- -and especially the flightless, bone-plate wings. None of them would have known that these ponies were once one of the dominant races of Equestria.

They were, of course, not alive, or not completely. They could not survive without the tubes and wires that connected to them, keeping the cells of their bodies marginally functional and dormant. Thebe had been perfecting the cloning process for decades, but her source material was simply too degraded. Much of it came from fossilized remains, or from the radiation-washed bones pulled from the Gloame. Celestia had indeed been thorough in their extermination.

The burrowing Pegasi, though, were only one of the two species that Celestia had deigned to remove from existence. Thebe had entirely given up on the other race long ago, however. With the Exmoori, she had viable genetic material, and the clones had formed well under the guidance of her magic. They had been perfect replicas of what had once been- -at first. They would always appear normal early on, but they would inevitably decline. Without fail, every Exmoori clone would collapse into homicidal rage. Their militaristic tendencies were pre-programmed into their very genetics; the clones would kill everything and everypony that came near them, including each other, until Thebe was forced to put them down. She had attempted the process hundreds of times, and every batch had failed. She had eventually given up her genetic samples to various private laboratories, but all they had produced were in-vitro genetic implantations, or at most deformed mutants.

The burrowing Pegasus squirmed slightly, and opened its eyes. One of its eyes was blind, but the other stared blankly. Its face shifted, as if it were trying to form facial expressions. They were, on some level, conscious- -even though their brains were ill-formed. They would wake up sometimes, and sometimes they would start screaming. Thebe hated the screaming ones, and always made a point to dispose of them properly.

She floated backward and looked up at the racks of hundreds of failed clones. She knew that there was really no point in keeping them, but something within herself prevented her from throwing them away. In her youth, she had been obsessed with restoring the lost two races. She was not sure why she had started, but the idea still held some romanticism within it. The idea that she, Thebe, could recreate what Celestia had destroyed, and undo the lesser alicorn’s greatest legacy.

Now, though, they would serve as a fitting audience. Irony, it seemed, liked to follow Thebe. She knew what needed to be done, and why. The incomplete, decaying clones seemed to understand too, and watched her knowingly.

“Well,” said Thebe, addressing her silent children. The only children she would ever be able to have. “I suppose I will be able to outdo Celestia after all.”

She hesitated for just a moment. Something within her felt strange, a like a memory from a time long passed, perhaps even a memory from before she had seen the truth of her existence. It hurt.

So she ignored it. Thebe activated the spell.

In the city of Baltimare, the city lights had just activated hours earlier, flooding the city with bright white light from the dome above. Ponies had already gone to work at their various jobs, but many were still walking through the streets, talking or purchasing groceries or supplies at the various stores, many of them altered in the last urban renewal cycle to resemble quaint and colorful structures.

Unlike many other cities, Baltimare had never grown into a full Megatropolis. In the past, it had been plagued with exceedingly high crime rates as well as racial tension, both of which had been spawned by the race-riots of the Second Choggoth War. For nearly a century, the city had been regarded as a dangerous wasteland of decaying buildings, drug addiction, and illegal firearms.

That era had long-since passed. It had now grown into a substantial city with a rich history, known for its peace and prosperity, as well as numerous medical centers that had grown up beneath the city’s famous lit dome. When ponies suffered from rare diseases or injuries that could not be healed elsewhere, they went to Baltimare for treatment.

Many of the pony residents worked in the hospitals. All of them were aware of the current outbreak. All across Equestria, ponies were falling ill with a mysterious disease. Their own hospitals had been packed with the infected who had been shipped in from all over Equestria. The disease had initially proven impossible to treat, let alone contain, but it the spread seemed to have slowed, which was fortunate. The Mayoral Council of Megatropolis 616 had just issued orders refusing entry of infirm from outer cities, so many new patients had been redirected to Baltimare. The hospitals were nearing capacity, and the work was grueling- -but the ponies of Baltimare were known for their caring, and their generosity. They would turn away no sick pony, and would deny none treatment.

Outside the hospitals, though, life continued as it always did. In no place was this more apparent than in Golem Park. The park sat in roughly the center of the city, a patch of grass and trees amongst the towers and brownstones of the city. The park itself had once simply been an undeveloped area known as a dumping ground, but through the hard work of all the ponies of the city, had become a thriving and beautiful sanctuary.

The park got its name from the titanic golem that stood in its center, looming hundreds of feet over the park. It had never moved since it had been placed there- -or, according to legend, walked there- -and it was largely overgrown with colorful flowering vines and turf that had taken hold upon its shoulders and head.

The fields beneath it were dotted with happy, smiling ponies. Among them were doctors on break, looking overworked but happy to be outside, as well as mothers with their foals. Fillys and colts ran through the fields, playing at the base of the golem. A young couple on a picnic giggled with each other in its shadow.

One particular filly was playing with a frisby. She ran toward the golem and caught it in her teeth, then threw it back to her laughing friends. She wished that she could have caught it with her magic, but her horn was still too small and stubby to use magic properly. Even though she practiced every night, her magic could still barely produce sparks, let alone perform a levitation spell.

As she began to move out of the golem’s shadow, she suddenly stopped. Most of her friends kept on playing- -except for the other one among them who was a unicorn. The filly looked around, and saw that all the unicorns seemed to have noticed the same feeling. One of the doctors had looked up from his coffee; the young mare on the picnic blanket had stopped kissing her coltfriend; a performer over by the tree line had stopped his juggling.

Then the ground began to shake. The filly was overcome with a powerful instinct to run, and she did. As she moved, she looked behind her- -and to her amazement, saw the six eyes of the golem aflame with scarlet magic. Then the it moved. She had thought that the stories were just make-believe, that the golem was really just a weird statue- -but it actually moved.

She stopped running, and watched as it stood, tearing the flowering vines that connected to its body out of the ground and stretching its arms. Then it took a step forward onto the ground, its clawed hoof nearly crushing the ponies below it.

The golem looked down at them all, as if were considering the world it had just awoken into. The ponies below- -though afraid- -did not know what to make of it. They had grown up around it, as had their parents, grandparents, and countless generations before them. The golem had watched the city grow around it, and never once moved- -they just could not bring themselves to be afraid of it.

Then it spoke. Its voice was booming and deep, but the filly had a strange sense that it was female.

“Engaging purge,” it said.

The last thing the filly ever saw was an eruption of red light from within the golem. Then, in an instant, she, along with the rest of the city, was reduced to dust.

In a site in the distant forest, the Grand Magus cried out.

“Grand Magus!” cried one of the dragon soldiers near him, a brown and gray male by the name of Smokebom. “Are you alright!”

“Did you feel that?” demanded Spike. The pain was not nearly as great as that which Goldmist’s eye had been producing as of late, but it was shocking none the less. “Did you feel that magic surge?”

“I felt something,” said a young female dragon. “But…what was it? An explosion?”

“Stay here,” said the Grand Magus. He spread his wings and spoke in fire, coating them in flame. With the spell in place, he rocketed upward into the high atmosphere, passing through the thick, white-sparking Order clouds that were permeating the area. He had defiantly felt an explosion- -and one from a familiar magic. Except that the location was wrong. He could not determine where it had come from.

Then he crested the top of the clouds, and understood. In the distance, he saw the columns of red light extending into the sky. There had not been one explosion, but many- -perhaps hundreds.

“No,” he said, unable to stop the tears. “Thebe…how could you? How could you have gone this far?”

In a decaying tower in a long-dead city, Toxic Shock suddenly felt a strange vibration running through his horn. His radio transmitter clicked loudly, and for a moment he thought that he was being contacted. Then his mind connected the combination of sounds and the sensation in his horn. He immediately raced to his computer and shoved the pieces back into place. He rammed the power supply cord into his body’s port- -and found that he was shaking. Even in a robotic body, he was shaking.

He activated the computer, and saw that his instincts had been correct. While waiting for a reply transmission, he had been watching the progress of cities that had taken the sick. For a time, he had been hopeful; although there had been no news of a cure, the spread had slowed and stopped. Now that hope was shattered. Every jurisdiction that had taken the infected was now nonresponsive.

“You idiots!” he said, slamming his metal hoof on the rusted desk. “If you had listened! If you had just listened!”

Toxic Shock recognized a purge when he saw one. He knew now the extent of his failure; that if he had just tried a little harder, if he had not let the quarantine break, this would not have happened. The weight of all the ponies that must have been culled now rested squarely on his shoulders.

Deep within the Eternal Forest, Lady Vale walked through the streets of one of the cities that surrounded her capital. She smiled and waved to the subjects below, who she was visiting. Their buildings were tiny, barely to her knees, carved from wood taken from the trees or built with tiny bricks. This city, of course, like so many of those that existed within her deepest sanctum, was populated by breezies.

The street that had been constructed through the center of the town was disproportionally wide for its buildings, but only because it had been built for her, as a path for her to walk through, to get meet the numerous breezie residents that dwelt within, who now came to their windows to see their Queen pass amongst them.

Ahead of her marched her husband, wearing a hat and twirling a baton to music that only he seemed to be able to hear as though the procession were a parade.

“Hello there,” said Vale, kneeling down near a small group of breezie children gathered at her feet. They at first seemed frightened of her blood-red eyes, but then they stepped forward cautiously. “Yes. Yes of course. There is no need for you to worry. The gohh are our friends now.”

Suddenly, there was a sound of breezies crying out, and a baton clattering against the ground. Vale looked to see that Discord had dropped it; fortunately, the breezies it had nearly landed on had moved out of the way.

“Discord?” said Vale, disapprovingly. “Now, I know you didn’t mean it, but you really should be more careful- -”

He turned, and she saw the uncharacteristic seriousness on his face.

“Hass,” he said, and space distorted. His rival appeared floating over the city like a dark cloud, its robes drifting beneath it in wind that nopony could feel. “You felt that, right? Please tell me you didn’t feel that.”

The yellow-clad being said nothing.

“On second thought,” said Discord, “don’t tell me anything. Because you can’t talk. Because I’m pretty sure you don’t have a mouth. And we all know how pretty I am when I’m sure…no. Not time for jokes. Find Snake. He’s probably in some tall grass or lurking in the background somewhere.”

“Discord,” said Vale, herself becoming serious. “What has happened?”

“Well…let’s just say we’re not going to have to send out nearly as many Hearthwarming’s Eve cards this year.”

In the city of Baltimare, several objects that had failed to be properly vaporized fell to the ground, landing in the wreckage below. Then they stood. The surge of magic had been unexpected, but useful. They had fed on it, converting it, using it to accelerate their pupation. Many had not been far enough in the healing process to withstand the process, and had exploded violently. Those that were near enough to their true and correct form, however, were able to survive.

Now each of them reached out into the wreckage, and into the supply of mass that their siblings had supplied for them. Each built a shell around themselves, and each turned toward the direction where the first of them was calling.

One, however, lifted its arm and pointed a finger at the golem that stared down at them. Before the golem could react, its source code was coopted. The fundamental control system was rewritten, and its six eyes shifted from red to pink and finally to white.

All across Equestria, the same was occurring. Many were understanding the true nature of their beings, of what it meant to be superior in every way to every other being. They were waking up. The time had come to begin construction.