Author's Note
Sorry if this makes any of you cry.
This a fan theory on how the crystals were made and how Twilight disappeared. This isn't official.
I'll miss you all too...
Twilight paced back and forth in the empty throne room, tears threatening to pour out of her eyes, but were fought back by her closed eyes. She took a short glimpse outside one of the tainted glass windows. All the royal guards were waiting outside the castle door, confused on why they were lead out for an ungiven reason. Spike was also outside, seeming to be crying. One guard was about to comfort spike, when suddenly, Twilight's friends ran through the crowd of guards, running faster than a cheetah being chased down by a lion. Twilight sighed. They're almost here. She thought, continuing her pacing. Ever since she had become a princess, she hadn't been able to visit her friends as often. Because of this, she arranged a meeting between all of them once a month. Today, unfortunately, was going to be the last day that would ever happen. a few seconds later, the throne room door burst open, letting all five mares in the room. They all looked at the tall alicorn with concern.
"We're here Twilight. Now what's the matter?" Applejack asked. "Why'd you call us here?"
"Is it a friendship problem?" Pinkie Pie chirped. "I brought friendship bracelets just in case!"
"Is it another villain we've gotta beat?" Rainbow Dash said, putting up her hooves as if she was about to fight.
"Or a d-d-dangerous beast?" Fluttershy stammered.
"Or is it just another ruffian to take care of?" Rarity asked. "If so, I'm don't think I'm ready to get my hooves dirty!"
Twilight calmed her friends before another could blurt out. She knew her friends would be confused, since she wrote to them on such short notice. Hesitantly, she explained.
"Thank you all for coming when I had told you. I know you're all confused, but I'll explain. So, I'm not sure if it's happened to Ponyville yet, but recently, a lot of my royal guard have been unable to fight, fly, or do magic. Even I've been having a few struggles. The only things I can do now are levitate objects, teleport and do simple spells. Other than that, I haven't been able to do much. What I think is happening is that magic is slowly disappearing."
"How am I not surprised?" muttered Rainbow, rolling her eyes. "What could it be this time?"
Pinkie gasped loudly. "What if Chrysalis, Tirek and Cozy Glow were freed and used those artifacts Cozy used to cause all this?! We're doomed!" Pinkie's comment led to the other mares starting to freak out, declaring possible explanations of how that could've happened.
"Girls, calm down," Twilight said calmly. "It's not those three. I checked, and they're still in stone."
"Then, what is it?" Applejack asked, just as confused as her friends.
"I'm not sure myself. It could be anything." the alicorn shrugged, picking up a book that was laid on the main throne's cushion with the magic she still had. "But, I think I found a way to fix it. I found a spell that can take the magic, flight, or strength from a pony, and transport it to a non-living object. I heard that it might be how magical artifacts are made." Twilight took out a small chest that hid behind the throne and opened it. The girls watched in awe as three very pretty crystals were taken out of the chest and placed in front of them. One was dark blue and was shaped a bit like a teardrop. Another was white and shaped like a circle. The last one was green and looked a bit like the wings of a pegasus. Pinkie resisted the urge to touch them. "I made these crystals just for this. If I can store the magic of a unicorn in one, the strength of an earth pony in another, and the ability of flight in a pegasus in the last one, I could put the crystals together and they would work together to keep magic in Equestria."
Rainbow looked at the three crystals in confusion. "So why did you bring us? Are we supposed to be the ones who give their magic?"
"Ooh! Ooh! I call dibs on giving my strength to the earth pony crystal!" Pinkie called, bouncing up and down and waving her hooves as if she was trying to get Twilight's attention. "I'm so nervouscited!"
"I guess I'll give up my flight." Fluttershy said, taking a step forward. "I'm not that good at flying anyways."
"Well, you see..." Twilight said, interrupting her friends' blurting. "It seems that the spell will turn the ponies in question into these sort of souls that enter these crystals, and the ponies don't seem to be alive." The girls stayed silent when Twilight said that.
"So...taking magic from ponies with that spell is the equivalent to killing them?" Rairty asked nervously.
Twilight nodded. "That's what it seems like."
"Then...we can't use that spell." Applejack said "Is there any other spell like that? Somethin' closer to what Tirek did? Ya know...taking magic but keepin' the ponies alive?"
"I'm afraid not." Twilight sighed. "You see, I-"
"Then I guess there's nothing we can do." Rainbow Dash said. "I'd hate to end up killing somepony."
"I guess we're gonna be living without magic." Pinkie whimpered. "But hopefully we'll be able to get used to it. Why don't I throw a 'we-don't-have-magic-but-we're-still-gonna-be-happy' party?" Pinkie was about to take her party cannon out of nowhere, but Twilight stopped her.
"There is a way we can use this spell." Twilight said, fighting the urge to cry. "We don't use it on another pony, but on me."
"WHAT?!" all five mares gasped in shock and horror.
"I would hate for ponies to loose their lives to this spell, and I already have characteristics from all three tribes. It's better than taking three ponies' lives."
"NO!" Pinkie screamed, running over to Twilight and hugging her tightly. Tears started to form in the pink pony's eyes. "You can't leave us! I won't let you!"
"Ya can't leave us Twi, ya just can't!" Applejack said, running up to the alicorn. "You're our best friend! If ya leave us, we all may not be able to stay together."
"Besides," Rarity added, also starting to tear up. "What about Equestria? If you're not there to rule, and Luster Dawn hasn't become an alicorn yet, who will take care of Equestria?"
Twilight smiled at the white unicorn. "Why have one or two leaders when you could have five? I trust you girls, and I know that none of you will let me down." Twilight picked up the spellbook in her magic and started to read the spell. Rainbow Dash smacked the book and it hit the ground with a loud thud.
"Forget magic! Forget Equestria! If a good future of Equestria depends on you dying, then I don't want it! I just want you to stay with us!" The blue mare hugged Twilight tightly.
"I agree!" Fluttershy sobbed. "Please Twilight! Don't leave us!"
Five sad mares surrounded the alicorn, begging her not to cast the spell. Every plea made Twilight even more emotional. Before she could burst into tears, She made a final attempt to convince her friends that this was the right thing to do.
"Girls...I'm just as sad as all of you, and I know how you all feel. But I have to do this. I'm scared that if Equestria falls, it could take all of you with it. The earth ponies make the food! If they loose their strength, it'll be harder to harvest. Equestria could starve!" Pinkie Pie and Applejack hung their heads. "The pegasi manage the weather! If they lost their ability to fly, who will bring the water?" Rainbow Dash and Fluttershy looked down guiltily. "And the unicorns bring magic! If there's no magic, how will the sun and moon move properly?" Rarity wiped her eyes with a handkerchief stifled a sob. "I'm not only doing this for Equestria. I'm doing this for all of you." Twilight gave a teary-eyed pleading look that made every one of her friends close to bawling. Pinkie stepped up and hugged the princess of Equestria, the element of magic, and most importantly, her best friend for the last time. The normally cheerful pony sobbed into Twilight's fur, her mane deflating like a balloon releasing air.
"Goodbye, Twilight. I'll miss you."
"M-me too." Rainbow Dash murmured, joining the embrace. Slowly, all six friends were caught in a group hug, crying like newborn babies.
"I'll miss you all, too." Twilight sobbed. Each mare slowly stepped out of the hug as Twilight picked the book up once again. She took a deep breath, knowing every breath after would most likely be her last. She light up her horn as she started to perform the spell. As her horn became brighter, the unicorn crystal glowed and floated in front of her. She flapped her wings lightly and the pegasus crystal followed. Lastly. She reared up, pawing her her front hooves in the air, and the earth pony crystal joined the other two. As the crystals became brighter, so did Twilight. Not just her horn, but her whole body. Soon it became so bright, her five friends had to cover their faces so their eyes wouldn't be harmed. Twilight could feel that she was becoming more weightless, and was being pulled toward the three crystals. She gave one last glance to her best friends. In her last moments, she reflected on her life. She had gotten so far. All the achievements, all the new things she learned, everything she's done for Equestria. It all had led up to this moment. Though Twilight was now not much of a solid anymore, she felt herself smile as she looked at her best friends.
Once Twilight's magic was given to the crystals, they linked together making it seem that they were all one piece. as the crystals made contact with each other, a loud and strong boom, similar to the sonic rainboom, roared loudly until it spread to the far ends of Equestria, knocking the five down in the process.
"Ugh..." Rainbow Dash groaned as she sat up. "My head hurts. If everypony okay?"
The other four mares sat up as if intoxicated, and looked around.
"What happened?" Applejack asked groggily.
"Girls, look!" Rarity exclaimed, pointing to another part of the room. The three crystals, now containing the soul and magic of Twilight Sparkle, floated calmly in front of the group of mares. They looked at the crystals in wonderment.
"I can't believe that those crystals have Twilight." Fluttershy whispered. "Do you think she can hear us?"
To test Fluttershy's question, Pinkie Pie walked up to the crystals pet them gently. "Twilight...?" Pinkie whispered. "Can you hear me? Are you there?"
Silence reined over the room. All the mares' eyes filled with tears. They tried to keep their cries quiet, but one by one, they all broke down. Fluttershy and Pinkie were they first to break the silence with loud, high-pitched crying. The two mares shared an embrace, crying into each other's shoulders. Rainbow Dash was next. She cried into Applejack's fur, as if using it as a tissue. Applejack tried to keep calm as she comforted Rainbow, but a few tears escaped her eyes, too. Rarity was the last one. She didn't even seem to care about how much makeup was on her face, she just bawled and bawled, and the five mares' cries echoed throughout the castle for hours.
Thousands of ponies, even a few griffons and dragons, gathered around Twilight's castle in Ponyville as five of the elements of harmony marched towards the castle. Spike looked at the three crystals that Rarity was holding in her magic and sobbed. He regretted following Twilight's orders to go outside while it happened. He knew that she didn't want him to see it, but he was still guilty for not being there in her last moments. Starlight Glimmer watch her friends trot by in saddness, wish that she could've been there too. The grown-up student six watched their professors walk with one of them being a crystal. They embraced and cried with one another. Before the mares entered the castle, a few members of the royal guard bowed down to them, accepting them as the new leaders, and showed respect to their old one. As the girls were let in the castle, they looked around and thought about all the great memories they had there. Now those memories will forever be in the past. Once they got to the room with the cutie map, Rarity put down the glass that contained the crystals in the center of the table and waved goodbye as they left the room. Altogether, they said in unison:
"We love you, Twilight. Goodbye."
