Twilight awoke. “Oh, what happen? Wait, where Starlight?” said Twilight, as she spun around, only for her face to widen in shock. “Wait where is the Castle Of Friendship? Where is anything?” She jumped off the map and started to walk.

Decaying trees were everywhere, the Everfree forest was way beyond its boundaries, and plunder vines covered every single tree. There was a distinct smell of ash, death in the air. It stank of it.

Twilight walked through the forest while trying to figure out what happened. ‘Everything looks so different. There are plunder vines everywhere, and the smell...ew! It’s nearly unbearable,’ she thought as her eyes started to tear. It was like there were onions everywhere. She kept walking, hoping that she would find some sign of what had happened, but as she kept walking it seemed to get her nowhere. It just seemed to go on forever, and looking up to the sky gave no help since the top of the trees were too thick to look through. This made it hard to tell what time it was, or even if it was day or night.

The alicorn just kept walking, hoping she would find something, anything. It eventually got to the point where she lost track of the path that led back to the map. She began to panic as she began to change from walking to jogging to full running in panic, trying to find her way out of the forest. But it just kept getting thicker as she ran. She just closed her eyes and kept running as fast as she could, her hope slowly fading away till...CRASH!

Twilight had crashed head-first into a signpost. She fell for a moment, before finally opening her eyes. “Ouch, my head,” she moaned as she got up and looked at the sign. Her hope was instantly restored upon reading that it was the signpost for Ponyville. Then things appeared to be getting better as Twilight found herself outside the Everfree Forest. “Oh good, I am glad that's over with now I just need to find some help, and I guess since I was in there at least a few hours, I need to fig-- ” said Twilight as she looked up at the sky. Her hope instantly turned to horror upon seeing it.

The Sun was in an eclipse with the Moon. The sky was no longer it's beautiful blue self. Instead, it was more of a burnt brown, with completely random hues of crimson red that striped across the sky like bands of tape.

Then Twilight looked past the signpost to see Ponyville. The place was in ruins and looked like it was abandoned long ago. “What happen here? Where is everypony?” said Twilight, “I need to find somepony, but there no sign of anypony even been here for at least years, but how can that be?”

The first place in town she came to was Fluttershy’s Cottage. “Ah, Fluttershy should know what is going on here,” said Twilight as she approached it. But there was nopony inside, not even animals. The place was covered in cobwebs and look like it had been abandoned as well. Twilight left the old cottage, confused, and went into town. “Maybe there somepony in town that can help me figure out what is going on.”

Twilight kept walking through town. “Maybe Spike can fill me in. He is probably still at Rarity’s.” She turned to the path the led to The Carousel Boutique, but when Twilight got to where the Carousel Boutique was, she felt even more confused. There was no sign of the Boutique anywhere. “That’s strange. It should be right here, but there's just an empty lot here. This is really confusing. Did everypony just leave, and speaking of it, I haven’t seen Rainbow Dash’s cloud home anywhere either. Maybe I can find more if I head more in town,” she said, hoping to find something to explain what was going on.

However, things got worse as Twilight came upon Sugar Cube Corner. “Oh no, Pinkie Pie? Mr. and Miss Cake,” she called as she ran in after seeing the place in shambles. Twilight was really worried for her friends now, but as she looked, she couldn’t see any sign of Pinkie Pie or even signs that Pinkie Pie even lived there. All signs of her from pictures to even the secret basement that Pinkie Pie had installed. Every sign Pinkie Pie ever lived there was gone.

Twilight began to think there was nopony left. “First Fluttershy is gone, then Rarity and Rainbow Dash, and now Pinkie Pie. I’ve got to find somepony. Where are all my friends?” She tried to think of at least where they would be. “That's it. Sweet Apple Acres. They could be there!”

******

Twilight ran as fast as she could, not looking to what else was different. She passed by it without even noticing, for if she had noticed that the Tree House Library was back, she would at least got some of her answers. Twilight kept running, also not noticing the pair of scaly green eyes watching through the window of the Library as she passed by.

Inside the Library were three little fillies, a yellow earth pony with a red mane, an orange pegasus with a purple mane and a white unicorn with a mixed purple and light purple mane. They were all wearing simple clothes. Beside them was a strange looking, scaly creature. “Who do you think it is?” Asked the yellow earth pony filly.

“Do think it is her?” said the orange pegasus filly.

“I don’t know. It could be her?” said the scaly creature.

“But how is she even here after what happen?” said the earth pony filly.

“Yeah, we all thought she was gone.” said the orange pegasus filly.

“I don’t know? I mean, I was there when it happened. She shouldn’t be here at all,” said the scaly creature.

“Maybe, it is one of those miracles you told us about?” said the white unicorn filly.

“You mean Magic? No, that's not possible. Magic is powerful, yes, but nopony can be able to use that much magic outside the empire,” said the scaly creature.

“But you can use magic,” said the orange pegasus filly.

“Yeah I can, but my kind of magic is not strong enough to do that. I don’t know if any spell is strong enough to bring somepony or anypony back from the dead,” said the scaly creature.

“What are we going to do?” said the yellow earth pony filly.

“We need to go tell the rebel forces,” said the scaly creature, then he pointed to the orange pegasus filly, “Scootaloo go tell the Cloud Rebels what we just saw. They have a standing alliance with the Dark Rebels. The Dark Rebel’s Leader will want to know about any info that pertains to her possibly being back.” He pointed to the yellow earth pony filly, “Applebloom go tell the Forest Rebels about we just saw, and maybe if you can get in contact with your brother, tell him too, being that he is part of the Dark Rebels as well.”

“And what about us, big brother? What are you and I going to do?” said the white unicorn filly.

“Sweetie Belle go tell your sister and the Cave Rebels what is going on, and I will keep my eyes out to make sure nopony spots you three leaving,” said the scaly creature.

******

Two hours passed before she saw any sign of the farm, then Twilight arrived at what appeared to be Sweet Apple Acres, hoping to find help. Instead, she found more ruins. Twilight was beginning to think that there was no hope at all. All her friends were gone, and all of Ponyville was in ruins.

But things were about to get worse as out of the sky they appeared. Five pegasi descended from the sky, landed and surrounded Twilight. At first, she thought they were Wonderbolts. But their uniforms had a different pattern on them. Instead of the sky blue, with a yellow lightning bolt, these uniforms that these five pegasi were wearing was more of a black and purple pattern on them.

“There is nowhere to run. You are surrounded,” one of the pegasi spouted. “Yeah give up,” said another. “There is no way you can fight us all by yourself,” another said.

“What do you mean? I'm not here to fight, I'm just looking for help, please just let me go I have to find my friends,” said Twilight.

Then one of the pegasi stepped forward, this one had a distinct orange and yellow mane. The pegasus mare stepped closer and took her hood off, “Please, Twilight don’t make this harder than it has to be.”

Twilight’s eyes widen as she realized who was right in front of her. “Spitfire?”

There she was surrounded by pegasi. She had no idea how to get out of this. Things had just gotten more confusing with the revealing of Spitfire being their leader. What was Twilight going to do? Well...fight.

Twilight tried to channel some magic to blast the pegasi away, but there was a problem, as she could not summon any magic. “What's going on here? Why is my magic not working?” said Twilight.

“Ha, ha, Twilight Sparkle,” said another pegasus as it stepped forward, this one light blue with a blonde mane. She took her hood off, and revealing herself to be Lightning Dust, “Did you forget that you can’t use any kind of magic including flying, without these,” said Lightning Dust as she revealed what looked like a dark amulet on her neck.

“Why are you wearing a dark amulet?” said Twilight in slight terror.

“Because all magic outside the Empire is nonexistent,” said Spitfire as she put chains on Twilight, “We even have to use these amulets to fly.”

“Wait, where are you taking me?” said Twilight as she was taken up to the sky. From above she could see that all of Ponyville was in ruins. All her friends and everypony she knew was gone. Tears fell from her eyes upon seeing so much destruction. Twilight then looked forward and in the distance, she saw that all of Equestria was in ruins.

The pegasi took her away. Meanwhile, Spitfire stayed behind for a moment and waited for them to be out of sight. Once everypony was out of sight, Spitfire grabbed out a piece of parchment and a quill and wrote a message. Then she left the parchment under a rock that had the symbol of the Wonderbolts. Afterward she left to join the others.

Later a light sky blue pegasus with a blue mane rolled over in a wheelchair, grabbed the parchment and read it.

“Contact ‘F’, tell him we found Twilight, alive.”

“SF,”

******

Meanwhile back in the Sky, Twilight was being taken up several mountains. She knew from the direction they were going, they were heading to Canterlot. Twilight was losing more hope with each town she saw in ruins. Things were about to get worse. She knew there was one more mountain before reaching the mountain that Canterlot hung from. As soon as they got to where she thought that mountain was, there was no mountain and instead there was a massive crater.

The crater was several miles in diameter, in fact, it was so massive there weren’t even other mountains around, just rubble. Twilight looked in horror of the crater, when Lightning Dust asked one the pegasi, “What is she doing?”

“She’s looking at her grave marker,” said one of the pegasi.

“Ha, ha, what are you remembering? Your big spectacular death in the third Dark War?” asked Lightning Dust.

“What are you talking about?” said Twilight upon hearing what they were saying about her being dead.

“You will find out soon enough, Twilight,” said Spitfire, as she finally rejoined the group. They continued their flight to Canterlot. At the far end of the crater, Twilight looked, hoping to see Canterlot, but instead there was a giant tower surrounded by more ruins.

“Oh finally, I was wondering if you had been captured by some rebels,” said Lightning Dust, “I mean, I've got no problem becoming the new leader of the Shadowbolts, but in order to do that I would to bring back proof that you died.”

“Well, I am not dead yet, and I am the only one who leads the Shadowbolts,” said Spitfire.

“Yeah, since Rainbow left, after she crippled her coltfriend, Soarin,” said Lightning Dust.

“You know that's not what happen,” said Spitfire in anger.

“She still left,” said Lightning Dust.

******

They finally arrived in Canterlot, or what was left of it. Empty buildings were everywhere - some even collapsed. On the signpost for Canterlot, there was writing carved into it. It read ‘Fallen Canterlot, the City of Dead Star’.

They got to the Tower and entered. Twilight was getting more worried with each second as she was pulled through the Tower’s front entrance, through to the top of the tower. At the top room, stood a glorious throne, covered in sapphires and rubies. Twilight was brought in and thrown in front the one sitting in the throne. “Princess Dead Star, we bring you a gift,” said Lightning Dust.

Twilight looked up in horror to see who was on the throne. The Princess was a light blue unicorn with an even lighter blue mane. It took Twilight an instant to realize it, but in front of her, was Trixie Lulamoon.

“Ah Twilight Sparkle, as you can see it is I, the Great and Powerful Trixie who rules this tower at the front post of the Empire,” Trixie bragged. “It has been a long time since we’ve seen each other,” she said. “Father will be most happy to see you alive,” she stepped off her throne. “While Mother, well you know how nightmarish she can be,” Trixie walked over to Twilight, lifting up her face with her magic and looked directly at her.

Trixie wore a black, skin tight suit and luxurious fluffy dark purple cape and hat. The star design was no longer of white stars, but of black, or dead stars, which seem to reference her new name being Princess Dead Star. And although she was called a princess, she was clearly no alicorn.

“Lightning Dust, contact General Dark Armor. Tell him that his sister has been found alive, meanwhile,” Trixie turned toward one of her guards that she had stationed with her, “Dark Sentry, take my ‘sister’ to a holding cell.”

‘What?’ Twilight thought. ‘Why is she calling me her sister? And who are this Father and Mother she was talking about?’ But before Twilight could figure out anymore, she was taken away by the pegasus guard.

The pegasus guard was called Dark Sentry, yet for some reason, she felt she knew this guard from somewhere, but she could not figure out who he was or where she had seen him before. As far as she could tell he had a blue mane, and that was it. The rest of his body was covered in black armor. She couldn't even see what color his coat was.

Dark Sentry took her down a few hallways and then to a cell and placed her in. Then the strangest thing is what he said. “Dark shines into the eternal night, but light shines into the eternal day,” then he walked off.

“Wait, what?” Twilight said as she was confused by the phrase. It was a phrase that made no sense. But that did not matter, for she had to figure out what was going on. Twilight began to ponder.

It only took a moment to figure out that Starlight’s attempt to go back in time and Twilight’s attempt to follow her, caused Twilight to fall in an alternate timeline that had been altered possibly by something Starlight did when she went through time.

And that in this alternate timeline, Twilight was now dead and Equestria was in ruins. But what alteration in the original timeline did Starlight make? Twilight had to figure it out, but there was just some info that she was missing, like why Trixie was calling Twilight her sister and who were these characters that Trixie was talking about - this Father and Mother? Plus, if Twilight was supposed to be dead, then how was she alive?

'Trixie said nightmarish, maybe this mother is Nightmare Moon. That would explain why the Sun is eclipsed, but who is this father?' Pondered Twilight as she sat in her cell.

Suddenly, there was a noise from down the hallway. Twilight looked outside her cell and saw a brown unicorn in a cloak, with a black and white mane and a beard, was walking over to her cell. She sat back down hoping the noise was over with. But then the unicorn walked over and said, “Dark shines in the eternal night.”

“What?” she said back. Then he walked away. Twilight was confused until she remembered the phrase. She looked to see if he was still there, and he was. “But light shines in the eternal day,” she said back to him.

At that moment the unicorn turned and gave the biggest grin, it almost seemed unnatural, which was not as surprising as the next part as he dropped a smoke pellet, causing smoke to fill the hallway. The cell’s door was knocked down and the unicorn stepped forward, removing his cloak and began to change shape. “It has been near a year since we last saw each other,” he said as he stepped in.

Twilight looked and although he looked slightly different with his now longer beard, Twilight knew that serpent shape, “Discord!!” said Twilight.

“Hello Twilight, I’m here to rescue you,” he said.

******

Author's Notes:

So like it has a different look. Each new chapter will roughly have at least two original chapters in it. Now this doesn't mean every chapter. There some chapters combined and some that are simple rearranged. Tried to reread what you can. That Plot really hasn't changed that much it just looks better now.