The sun was out later then usual and Twilight Sparkle was doing some on the field research, she wanted to study the tree of harmony and learn more about it's secrets. She read all the books she could about it but found almost nothing. She didn't really care about going places but she got the idea from her friend Sunset Shimmer, Sunset told her she was a hands on kind of girl, always going out onto the field and such. She had decided to take matters into her own hooves and study the tree.
She asked Celestia to keep the sun up at least an hour or so, she needed light to work after all. She had a saddle bag full of supplies and she was ready to learn. Spike was following right behind her as usual, he followed her everywhere even when she didn't want him to. She loved him like a little brother/pet.
"So why are we going out this late?" Spike asked as they walked through the forest. "And tell me again why the sun is still up?"
"Because I want to study the tree of harmony Spike, and I asked Celestia to keep the sun up an extra hour so I can get everything set up for my late night studies." Twilight explained for the tenth time. "Come on Spike."
They went to where the tree was and Twilight's eyes grew wide. "What in Equestria?"
The tree of harmony was not there just a blue stump. Spike went over to it and waved his hand over the stump. "The tree is...a stump!"
"This can't be! The tree of harmony can't be gone! It's the tree of harmony! Without it we don't have the elements...or any means to defend Equestria!" Twilight dropped her saddle and dashed over to it to the stump. "This is bad Spike, this is really really bad!"
"Calm down Twilight, it's just a tree." Spike looked at her like she was overreacting.
"You don't understand Spike, the tree of harmony is the heart of Equestria, it gave us the elements. Our rainbow powers...even our home!" Twilight told him getting into a panic.
"So are we going to lose our home again!?" Spike asked shocked.
"I don't know!" Twilight shouted making Spike jump from that. "This is going to be bad no matter what..."
"Hey!" A voice came from the outside of the small cave. "Get away from our daddy!"
Twilight and Spike turned to see two fillies at the entrance. "Huh? Who are you girls?"
They walked in revealing to Them they were real life alicorns. One of them was white with rainbow hair and pink eyes. The other was a purple alicorn with purple hair and pink highlights she also had purple eyes. Twilight was shocked to see two filly alicorns. "Who...who are you girls?"
"That doesn't matter. Get away from our daddy!" The purple alicorn said getting in her face. The white one went over to the stump and gently pushed Spike back.
"Your daddy?" Spike asked confused. "What are you talking about?"
"This is our daddy!" The white mare spoke. "You can't hurt him."
"Your daddy is the tree of harmony?" Twilight asked. She couldn't believe what she was hearing. "That's just silly. A tree can't be a parent."
"Well it is, right sister?" The purple one pointed out.
"Actually…we don't know." The white mare said turning to the stump. "All we know is the tree gave it's life for us to be born."
"Gave it's life? What are you talking about? Can you start at the beginning?" Twilight sat down on the ground as she asked.
The purple mare sat down on the stump as did the white mare. The purple mare didn't really know what to say so the white one spoke for them. "I...I mean we woke up in some strange pods, all I saw was white. Then a voice in my head telling me, showing me things how to walk. Talk. Who I was, what I was. The pod opened after awhile, to be honest I don't know how long we were in there but we were in there together. So on the family note we know we're twins, but that's it."
"You both were in a pod...that's strange." Twilight pondered. From her story she could see why they would be so lost. "Have you two been living in the forest ever since you woke up?"
"It's been three months so yes." The mare said with a nod.
"I'm lost." Spike admitted. "Can you explain Twilight?"
Twilight had sparkles in her eyes at this point. She understood everything they explained. "I get it. The tree made them, their children of harmony Spike! These girls were given life by the tree itself. All these answers are raising more questions. I want to study you girls!"
"Study us?" The purple mare looked at her confused. "What's that mean?"
"Well first let's introduce ourselves." Twilight said happily. "My name is Twilight Sparkle and your names?"
The mares looked at each other for a bit and then back at her. "Names?"
"Yeah. My name is Spike, everyone has a name." Spike pointed out. "You have to have one so we know who you are."
"We don't have names." The purple one admitted. "We just call each other sister."
"Is sister a name?" The white one asked.
"Amazing, your like new born fillies with older bodies, I have to take you both home with me!" Twilight's science side was showing as she needed to study them.
Twilight stood up and offered them a hoof. "So how about it? Would you let me work my magic and allow me to study you both?"
"Would you….name us?" The purple one asked.
"If you want me to yes." Twilight nodded.
"What do you think sister?" The purple mare turned to her sister.
"Well...okay, but what do we do about daddy?" The white mare asked.
"We take daddy with us!" The purple one said getting off the stump.
"That sounds good." The white mare got off the stump as well. Their horns started to glow when Twilight grabbed them both.
"Hold on girls, you shouldn't do that." Twilight explained. "If you pull the stump out it might completely die, if this has even a little magic left it can grow back. We need this tree."
They stopped and nodded. Twilight then picked them both up and put them on her back. "Come on, you won't have to live here in the dark and damp forest with all these monsters anymore."
"How did they survive here for three months again?" Spike asked as they walked out.
"We found a bunch of apple trees just outside of the forest so we have been picking them." The white one answered.
"Wait…apple trees near the forest?" Twilight got worried from this. "Applejack is going to be really mad when she hears about this."
"Applejacks? Is that some sort of food?" The purple mare asked.
"No she's a friend of mine. You'll meet her soon enough. But first lets get you to my castle so we can study!" Twilight picked up the pace excitedly.
Spike looked at Twilight concerned. He never saw her this excited about something that could hurt all of Equestria. The tree was gone and she's calling these homeless probably delusional fillies. "Are you sure about this Twilight?"
"What do you mean?" Twilight looked at her little friend.
"We don't know if their telling us the truth. What if their lying?" Spike asked not realizing they could hear him.
"What's lying?" The white one asked.
"I think you have your answer there Spike, they don't even know how to lie and even if they did they have no place to go." Twilight answered.
"Well okay then, if that's what you want to do." Spike asked still lost.
Twilight took them to her castle and they got off her back when they went inside. "Okay girls let's get to work."
Twilight showed them into a room full of weird looking devices, they looked at Twilight worried and hoped she wasn't going to do anything weird to them. "Um...is this safe?"
"Of course it is. I would never try and hurt you girls. Just sit down and I'll do the rest okay? I want to make sure my theory about you girls is right." Twilight said sitting the girls down on some tables. Spike looked at them and rolled his eyes. Twilight always got like this sure, but doing weird stuff to kids wasn't normal for her.
"Are you sure about this Twilight? Their just homeless kids looking for attention." Spike said. He had a feeling this was just a bunch of hay.
"Why would you think that Spike?" Twilight looked at him confused. "Their alicorns for starters, baby alicorns that's rare. It's not something you can make up."
"Yeah but maybe their fake wings or horns, maybe their lying, I mean they believed a tree was their dad and they woke up from a pod. That's clearly a sign of delusion right?" Spike explained.
He made a good point, Spike was normally right about these things. Maybe she did jump on this too soon? Twilight went over to the purple one and felt her horn and then her wings. "Could you two show me some magic and maybe flying around for me?"
The white one nodded and she flapped her wings flying into the air. The purple one focused and her horn glowed lifting multiple objects around the room. Twilight clapped happily at this. "This is amazing, real alicorn children!"
"Why would alicorn children be homeless that doesn't make any sense. All alicorns are royalty in Equestria." Spike pointed out again.
"True but that's why we're studying them." Twilight said as she got to work. She took a little hair from their manes and worked on a DNA sample as she tested them in other ways. After hours of testing it seemed like everything was normal for them, they were truly alicorns, their magic was powerful and they never seemed to get tired from using it. And they could fly fast, probably faster then Rainbow Dash with some work.
Spike went upstairs to get something to eat and Twilight's DNA test was finished. "Okay let's see what the readings say."
"She's a little...weird isn't she?" The purple one whispered to the white one. "What's DNA even mean?"
"I don't understand ether, maybe she's trying to come up with names for us?" The white one said with a smile.
"Oh that makes sense." The purple one smiled at this.
Twilight was really testing to see who their parents were. Clearly it couldn't be the tree of harmony. She knew the tree was gone but she also knew it could grow back in a few hundred years given some care, but she had to know why these girls truly believed they came from the tree itself.
She couldn't help but think there was more to all this. Her thoughts went back to what she said before. "Children of harmony." She didn't realize what that really meant at first, it was a theory but she believed the tree did to something to these girls. If she believed what the twins told her they were created by magic from the tree itself. She knew the elements of harmony were powerful but she didn't think they could create life itself. If friendship magic could do something so powerful what about other forms of magic?
If they had the same DNA as the tree she knew her theory would be right. The results finally came in and she looked them over. She stopped and looked at it again. "This..this can't be...I don't understand..."
The children looked at her as she kept reading over and over again. "What are you reading?"
Twilight then showed them the paper. "Look at this. Your DNA matches that of our princess Celestia!"
The children just looked at her confused. Twilight's test said that they shared DNA with Celestia, they were Celestia's children, she had no idea Celestia had kids. But that just made her more confused on why they said their father was a tree. "Your mother is Princess Celestia, that is huge!"
"You mean we have a mother?" The white one asked flying excitedly. "Can we meet her!?"
"Give me a minute." Twilight ran upstairs to talk to Spike about sending a letter to the princess, the purple mare looked at her sister. "Sis? Is it true? We have a real mother...then what about daddy?"
"I...I don't know, daddy told us everything we needed to know on how to live. But nothing about our family or all that other stuff. All I can recall is some magic around us and then we were born." The white one pointed out.
Twilight came back down after she got the letter sent and smiled at the little ones. "Would you two like a snack?"
They both nodded and Twilight took them upstairs into her kitchen, she was feeling really attached to them for some reason to be honest. She set out some bowls and with her magic took out some healthy food like carrots and celery. "Eat up girls."
The purple one happily ate while the white one looked at Twilight. "Um...you said you'd name us. Are you going to do that soon?"
"Oh right." Twilight almost forgot about that. She thought about it and smiled. "Okay...your name will be….Shining Star Sparkle. I like the name Shining, my brother's name is Shining Armor. And for your sister...how about Dusk Sparkle."
"We're both Sparkle?" The purple mare asked.
"That's my last name. All the girls in my family are Sparkles. My mother's name is Twilight Velvet Sparkle. We normally use the first two names though. So Shining Star Sparkle will be just Shining Star." Twilight explained.
"Ohh, I like that name! Shining Sparkle Star!" The white mare said before eating.
"No it's Shining Star silly. I'm glad you like it though." Twilight smiled and sat with them.
"Dusk Sparkle. That's a good name, right sis?" Dusk Sparkle asked her sister.
"Are you kidding, that's a much better name then what I was going to call you!" Shining Star nodded. "I was going to call you Moon or something silly like that."
"I was going to call you Rainbow cloud myself. Haha!" Dusk Sparkle laughed which made Shining Star laugh with her.
Twilight just giggled to herself at this. She remembered what it was like to be a child herself. "So do you two like books?"
"What's a book?" Dusk Sparkle asked.
"This." Twilight used her magic to bring over a book. She had books all over the place so finding one wasn't hard. "You read it to learn things."
Twilight placed the book in front of them, for the little alicorns it was just a block of letters. "O...n...c...e?"
"U...p...o...n….a…." Dusk Sparkle and Shining Star looked at Twilight completely lost.
"Time." Twilight finished for them. "You girls can't read?"
"We've never seen a book before." Shining Star answered.
"Right, you have the bodies and skills to survive the wild. But being in a town would be like being in another world for you two...well then I'll teach you!"
"You will?" Dusk Spark smiled. "That sounds fun!"
"I love reading already!" Shining Star jumped.
Twilight took them to her living room where she sat down on a bean chair with a bunch of books around her. The two filly twins jumped on both sides of her and cuddled up to watch her. "Okay so this is a learning book, it's simple but it should help to start you off."
The twins were already reading the book and having fun. "A is for Apple. Oh I eat those!" Dusk Sparkle pointed out.
"B is for Bubbles! Oh oh, I saw some in the pool, you know under that rock!" Shining Star said happily.
"You two are really fast learners." Twilight mentioned as she watched them quickly learning. She was impressed on how they were able to master the alphabet in five minutes and quickly went to reading much harder books.
They were now reading the elements of harmony book that Twilight saved when she was still a student. She was amazed how smart they were. She realized they were not only special alicorns they were gifted alicorns. "You two are already reading advanced levels? But you just started on the beginning books. It took even more a couple days to learn all of that."
The twins were completely absorbed in their book when Twilight heard a knock on the front door. "Oh that must be Celestia. I'll be right back."
She stepped away when Shining Star spoke. "Okay mom, hurry back this is really fun."
Twilight stopped and smiled at this. She never thought of herself as a mother type but she felt a connection with these twins, something she couldn't explain. She barely even knew them to.
Twilight went to her front door and opened it. Sure enough Celestia was waiting right on the other side. "Twilight? You told me you had news about some children?"
"Yes I do princess Celestia. Follow me." Twilight led her downstairs. She took the DNA results and showed them to the princess.
Celestia looked it over and not surprisingly looked worried. "I...I have children?"
"Somehow the tree of harmony before it died gave life to these two. I don't know what happened or why but my studies show their your fillies. One even looks a lot like you." Twilight explained.
"And I assume the other one looks like you?" Celestia asked suddenly.
"What do you mean?" Twilight looked at her confused.
"Your DNA results shows my DNA...and yours." Celestia pointed out on the chart.
Twilight looked at the chart and her jaw dropped. She couldn't believe she missed that. "That's...impossible!"
"Normally yes, however Twilight I think I can explain. When I was younger me and Luna would visit the tree often, then when Cadence became an alicorn she would visit it as well. And then you came into your alicorn powers and did the same. The tree of harmony was old and powerful. Over ten thousand years old by the time me and Luna found it. The tree has been around our alicorn magic for a long time as well. So one way to explain this is the tree used our magic to create the fillies before it died. They would be-"
"Children of harmony!" Twilight said finishing her sentence. "I can't believe I didn't see that earlier, I thought I was just being clever with that title."
"So in a way their my children and yours." Celestia pointed out. "Which...is a little more then odd..."
"I have children...with THE Celestia?" Twilight blushed deeply from this, it was actually one of her fantasies believe it or not to be with Celestia but she never thought something she dreamed up when she was younger would be true.
"This is very concerning, I never even thought about what I would do if had children." Celestia explained.
"So...what can we do?" Twilight asked.
Celestia thought about it. "You enroll them in school of course, for now just pretend their your nieces or something and their staying with you for awhile."
Twilight nodded. Who would believe twin alicorn children were hers, they didn't look like babies so that was going to be weird to explain. "Okay, I can get them in the same school as Applejack's sister by tomorrow."
Celestia nodded and they went back upstairs. Twilight only had one question now. "What will you do about them?"
"I'll come and visit from time to time when I can, it won't be easy but I want to study them closely something about all this seems...unsafe." Celestia said.
"It is very odd to be honest, I wonder what Melody Bloom or Starlight will say?" Twilight said following Celestia into the room where Twilight left the twins.
The twins were fast asleep by the time they showed up, it had been a long day and they were just fillies after all. "Oh...I'll get them to bed, thanks for coming over Celestia."
Celestia nodded. "It's always a pleasure to see you Twilight, even this late at night."
Twilight had forgotten that it was in the middle of the night. It was actually passed midnight by now. Twilight used her magic and lifted the sleeping fillies onto her back. "I'll take them to bed now."
Celestia smiled and looked at the sleeping children, she was amazed Shining Star looked so much like her. Twilight wasn't making anything up like she first thought. She had a lot to think about.
Twilight went to her bedroom as Celestia went home, Twilight didn't have any extra beds so she used her magic to lay them down on her bed. She put the covers over them and they cuddled up together enjoying the warmth. Twilight let out a yawn she didn't know she was holding in and joined the fillies in bed. She noticed Spike was already asleep and she slowly drifted to sleep.
Celestia teleported herself back to her room in Canterlot, she couldn't believe it. She had children...and with Twilight. If the world found out it about this. Rumors could hurt a lot more then just herself. What would ponies say if they knew about them? Twilight was her student for a long time. How would she even explain the fillies? Something foolish like "Magical tree babies."?
This was going to be hard to accept or even explain. All on her mind was those fillies. There was something more to all of this they were missing. She sighed and went to bed trying to not think about it.
The next day in Ponyville Twilight woke up to see the fillies were gone already. "Girls?"
Twilight noticed that Spike was gone as well. She got up and heard some laughter right outside and went to her window to check it out. She saw the twins playing with Spike, well actually it was more like Spike was chasing them around trying to get them inside.
"Hey! You two can't go out without Twilight around! Come on!" Spike shouted trying to chase them.
"Come on Spike, fly with us!" Dusk Sparkle spun around with Shining Star. "It's fun!"
"I can't fly though!" Spike shouted.
"That's okay, here!" Shining Star's horn glowed and shot a beam at Spike hitting him.
"Oh!" Twilight saw this and quickly ran outside. "Spike are you okay!?"
She didn't see Spike at all, there was only a soot mark where he was. "Shining Star what did you do!?"
"It's okay Twilight, I'm up here." She heard Spike's voice above her. She looked up and saw Spike with dragon wings flying with the twins. "Check me out!"
"Wings?" Twilight was shocked to say the least. "But your a baby dragon, how did you get those!?"
"Magic!" Dusk Sparkle pointed out.
"Shining Star used magic to grow wings on me!" Spike explained. "This is awesome, why haven't you given me wings before Twilight?"
"I never really thought about it before." Twilight admitted. "But this kind of spell isn't easy, how did Shining Star cast it without even trying?"
Shining Star flew around doing twirls and playing with Dusk Sparkle. Twilight cleared her throat and focused. "Girls? Can you come down here for a minute? I have something to tell you."
They floated over to her and landed on the ground. Their little attention spans fully focused on her. Twilight sighed and spoke. "Okay girls, Princess Celestia would like you two to go to Canterlot and attend school there."
"What's school?" Dusk Sparkle asked.
"It's a place you learn about life and just about everything else. Make friends and all that." Twilight explained.
"That sounds fun!" Shining Star said happily. "Let's go!"
"This is a really big school, it's one of the most difficult schools to get into. Are you two sure you want to go there? I mean I don't want to force you." Twilight said.
"Can we go see what it's like and then decide?" Dusk Sparkle asked.
Shining Star nodded. "I hope I'm good around people."
"What do you mean Shining?" Twilight looked at her confused. She didn't think Shining Star was shy due to how much energy she had.
"Shining Star is actually pretty shy around new people." Dusk Sparkle admitted.
"That doesn't make much sense, when I talked to you two it seemed like you were the shy one Dusk." Twilight pointed out.
"Well we're both shy to be honest. Your just...different." Shining Star added. "You...feel like a mother to us."
Twilight smiled at them. "Let's get going you two, I just now you'll love it here."
Dusk looked at Spike who was flying around with his new wings and enjoying it. "Sorry Spike play time is over."
She cast a spell and Spike's wings vanished making him fall to the ground with a loud thud. "Oof! Hey I wasn't done yet!"
"Come on Spike, don't be so lazy. Go wake up Starlight, we have a busy today ahead." Twilight said before walking with the fillies towards the school.
Spike sighed and went back inside, he would honestly miss those wings. Twilight used her magic and lifted the girls onto her back so they would get there faster. She wanted to make sure they were safely at school before going on with her studies.