Twilight woke up with her head on a guillotine, her body barred with more magic bars, her horn incapacitated by a curse. Twlight's breathing pace quickened. The feeling of impending doom had set in and she began to have a panic attack. Then she looked up and saw her friends before her. "Guys… you… you need to get me out of here! They'll kill me!" Twilight pleaded.
"Not 'they' Twilight, 'we'. We are the ones who asked for your head." Pinkie Pie said, and not even her naturally bouncy voice could make the situation seem any better. Twilight looked at Pinkie, tears welling in her eyes. She closed them and let out a loud cry. She was so confused, she simply didn't understand any of what was happening.
"We're… awful sorry, Twi. But you…" Applejack began, but she started sobbing and she couldn't finish her sentence.
"Twilight, you end up killing every pony. Even the Princess. All of Equestria is doomed if you live. I'm sorry…" Rarity continued.
"Spike, please, tell me this is some kind of joke!" Twilight said, hoping her trusted dragon companion would come to her rescue. He didn't reply, he only looked away from her.
"Twilight, we'll miss you… And you know that we love you. I hope that you can forgive us, we're only doing this because we have to. It was the Princess's final request." Fluttershy said, reaching for the string that would trigger the blade to fall. Rainbow Dash took the string from Fluttershy's mouth, relieving her of the burden. Fluttershy joined the other ponies, who were crying off to the side, looking away from Twilight.
"Girls…" Twilight uttered. Rainbow Dash put on a brave face and tugged on the string, averting her glance until it was over. She looked back and saw for certain that Twilight was dead. They remained in the room and comforted each other as they wept.
"It's all over…" Applejack said.
When they were finished mourning, they returned to Celestia and were sent back to future. What they saw was the opposite of what they had expected.
Everything was much, much worse than how they'd left it. Ponies lay dead in the streets, buildings and trees were on fire, and screams were audible from every corner of the land. Shadowy figures flew around in the skies walked about on the ground, patrolling the land for more victims. Up where Canterlot should have been rose a dark spire that shot above the storm clouds and up into the black sky.
"I thought that by killing Twilight, everything would go back to normal… What… What happened?" Applejack questioned. She soon noticed her mistake for at the sound of conversation, a team of shadows flew down and grabbed them, dragging them straight to the spire. Each one of the ponies was regretting killing Twilight. It had made everything worse, and now they were without their best friend.
When they arrived at the Spire, a familiar black pony with flaming hair was waiting for them. Sombra laughed maniacally, just like evil Twilight had and then he said, "Well, well, well, if it isn't my favorite ponies. You know, if it wasn't for all of you, none of this would have been possible."
"What do you mean, Sombra? Was it your plan all along to have us kill Twilight?" Rainbow Dash yelled, her pride diminished and her hatred fed.
"Well of course it was. Oh, and you did so much more. You know that the 'me' that you destroyed at the Crystal Empire wasn't me, but merely my shadow! I needed Twilight to use dark magic so that I could take over her body and regain my strength, so I could reappear once again in my own body, with my full power! Once you killed her, you released me, and I was able to kill Celestia. With those two out of the way, I had no one to oppose my rule!"
"That's not true!" Rainbow Dash screamed. "Princess Luna will stop you!"
"Stop him?" Another pony's laughter came from somewhere in the room. Out of the shadows stepped Princess Luna, dressed now as Nightmare Moon. She joined Sombra at the throne. "We are Sombra's queen! Did you really think that we wanted to be thy friends? Ha! We have always been evil, and we shall always be!"
Sombra laughed with her, the ponies shivered with fear.
"Princess Luna was always Nightmare Moon. She merely put away that evil for the sake of her disguise until I and my Crystal Empire would return. And now, we rule the whole of Equestria! And now you shall share the fate of your friend!"
Spike and the five ponies looked at each other, ashamed of what they had indirectly caused. Now, it really was all over.