We're WHAT!? (Rewritten)
Sunset mind was reeling and she felt as if somepony had dropped a ton of bricks on her. 'Princess Celestia.....my mother? Twilight's mother?! Then....we're-'
Twilight and Sunset exchanged a glance, coming to the same conclusion. They then looked at Princess Celestia and Princess Luna. They both opened their mouths, but no sounds came out. Neither could comprehend what they had heard.
Princess Luna wore an expression of understanding while Princess Celestia wore an expression of pure sadness and grief. Princess Luna was surprised that neither Twilight or Sunset was shouting accusations, or questions in the former's case.
Twilight snapped out her shock first. Seeing Princess Celestia's expression, she knew it was true. And to think, she had been looking forward to this meeting! In spite of her confusion, she found her curiosity getting the better of her.
Sunset couldn't believe it. She felt anger well up in her. All this time, she had trusted Princess Celestia! She thought she was the one at fault coming into the meeting, but Princess Celestia was at more fault than her! And to top it off, she had even had both of them as her students! Couldn't she have had said something then instead of now?!
"Princess Luna, i-is it true?", Twilight asked shakily.
Princess Luna opened her mouth to answer, but Sunset cut her off. "Of course it's true, Twilight! Think about it! She had both of us as her students! She acted like our mother! She saw us as her daughters the entire time! Even after she abandoned us! I don't she even thought about our feelings!"
"SILENCE!" Princess Luna yelled in the Royal Canterlot Voice, fanning out her wings for emphasis. If not for the sound-proof barrier, the glass within 100 meters would've shattered. Unfortunately for Twilight and Sunset, the Royal Canterlot Voice nearly burst their eardrums and Sunset was stunned by the intensity of Princess Luna's command.
Princess Luna continued, but without the Canterlot Royal Voice. "This is why I came along. I knew there would be some....difficulties explaining this to you two. Ask ahead, but no accusations or insults about my sister." She glared at Sunset at that last part.
Princess Celestia had not moved from her spot and it didn't seem like she had heard anything. But as Princess Luna finished her instructions, (if you could call them those) she looked over at Sunset and Twilight, the former wearing an expression of anger and the latter an expression of pain.
Their expressions reminded her of how much she had kept from them and also events she would rather forget. Sunset's expression matched her mood back when she was denied ascension. Twilight's expression reminded Princess Celestia of Cadance's wedding rehearsal where everyone abandoned her to comfort Cadance, who was Chrysalis in disguise. She had failed them so many times before, yet her biggest mistake was not telling them sooner.
Her heart twisted with regret at the sight before her. She couldn't hold back the waterfall of tears any longer.
Sunset's and Twilight's expressions changed to disbelief as they saw Princess Celestia crying. Sunset had never seen the regal diarch cry before while Twilight had only seen her cry twice before, and one of those instances was the result of a flashback potion. Never had either seen Princess Celestia so grief-stricken.
Sunset almost felt sorry at what she had done, but then the image of her and Princess Celestia standing side by side when she was a mere filly slipped its way into her mind. 'I'm not wrong. She did always see us as her daughters! Even though, we didn't! Obviously, she didn't care for us enough to take care of us herself!'
Twilight gazed hesitantly at Princess Celestia, her supposed birth mother before opening her mouth to ask a question that bothered her very much. "Prin-"
"Twilight, I don't think it's appropriate to address her by 'Princess' any more," Sunset said sarcastically with a sneer. Twilight recoiled at the venom in the remark. Sunset was sounding like the bully she used to be at CHS! She composed herself and gave an uncharacteristic smirk.
"Well, if you have any problem with it, why don't you be the one to call her by the appropriate title?," Twilight retorted before turning to Princess Celestia. Sunset scowled at the comeback, unable to come up with anything else. The smirk disappeared from Twilight's face as she asked, "Princess, why did you send us away? Couldn't we have grown up in the castle by your side?"
Princess Celestia flinched slightly, as if Twilight had attacked her. She said in a barely audible voice, "My daughter, I was afraid for your safety. If I had raised you myself, many enemies would see it as an opportunity to attack Equestria. And also because of all the turmoil it would cause in the country."
Twilight wasn't satisfied with that answer, and she felt that Princess Celestia was hiding something. She didn't push it though. It would eventually come up. Sooner or later.
Sunset had no such qualms. She asked in a loud, demanding voice, "Why can't you tell us the truth?!" She stomped her hoof, not caring that the pony in front of her was the co-ruler of Equestria. "You've kept this secret from us for far too long. Even when you didn't raise us yourself, we were your students! How were we supposed to be in any less danger than if you did raise us as your daughters?!"
Sunset's words infuriated Princess Luna. No pony had ever dared to yell at her sister. But in her somber state, Celestia gave her a glance that warned her not to use the Royal Canterlot Voice again.
While Sunset was still fuming, Twilight asked uneasily, "Princess, why did you send me on so many dangerous missions if you truly cared for my safety?"
Princess Celestia hesitated slightly before answering. "I sent you on the missions to see whether or not you were ready for ascension, my dear daughter. I would never let you truly get hurt. I was always watching from the heavenly dimension you were given ascension."
"So...you would've intervened if I was in danger?", Twilight asked hesitantly.
"I would have," Princess Celestia said as she nodded solemnly.
Visibly relieved at that statement, Twilight asked another question that had been nagging her. "Princess, who's our father?"
There was a stone silence.
Princess Celestia and Princess Luna seemed to be rather on edge with the question while Sunset merely raised an eyebrow at the question.
Finally, Princess Luna answered for her sister. "Ahem. You see...your father is well...uhm...the ruler of another...well...Equestria."
Twilight nodded and closed her eyes, putting two and two together. Her eyes shot up as she realized what Princess Luna was getting at. Her mouth gaped, but no words formed.
Meanwhile, Sunset was immensely confused. Another Equestria? What?!
"Could somepony explain to me what's going on? And how this relates to our father?", Sunset asked confusingly, unable to hide the curiosity of her voice.
Twilight turned to Sunset, apparently getting over the shock of...whatever she was thinking and delved into the adventure they had through the mirror and into the alternate world.
"....we returned to this world, the mirror pieces were destroyed" Twilight wished Princess Celestia wasn't there so that she could tell Sunset "and everything more or less returned to normal," Twilight concluded.
One could practically see the gears turning in Sunset's mind. She obviously must've come to the same conclusion as Twilight, for she wore the same bewildered blank look Twilight had. She exchanged a glance at Twilight, who nodded, and they looked at the two diarchs.
Sunset started off. "So you're telling us that our father is-"
"-King Sombra from the alternate universe?!", Twilight finished.
Princess Celestia merely nodded. The two young mares gaped. Sunset nearly forgot about her anger at Princess Celestia in the light of this information.
"Er...can I ask something?" Sunset asked warily.
"Of course, my daughter. Now, what is on your mind?"
"First of all, don't call me your daughter. As for the question, do our families know about us being your daughter?" Sunset stated hotly.
Twilight stiffened. No. If Princess Celestia says that they knew, I have some harsh words to say to Shining! Princess Celestia's voice brought her back to reality.
"Well, your parents knew that you were adopted, but that's all. I had disguised myself as a young unicorn mare when I gave you away, so they wouldn't know that you are royalty. And no, Twilight, your brother doesn't even know that you were adopted." She had said that last statement with a hint of knowingness.
Twilight didn't even ask how Princess Celestia knew about her thoughts. She wouldn't be the co-ruler of Equestria if she didn't know about such things.
Sunset merely snorted and said in a rather disgusted voice, "Oh, so you had to disguise yourself when you abandoned us. Shame that even the ruler of Equestria hides her secrets."
Princess Celestia flinched. Princess Luna could barely take anymore nonsense from Sunset. If not for the fact that her sister had specifically warned her not to use the Royal Canterlot Voice, she would've used it a long time ago.
She composed herself and glared at Sunset before speaking. "I know that you must feel like your life is a lie, but that is no reason to have such a demeanor towards my sister. She did what she thought was best for you two. Believe me, it came as a shock to me as well."
Sunset had an expressionless face. Her voice was quiet but it held all the venom in the world. "The best thing she could've done for us was tell us the truth."
Deciding to cease the eerie mood, Twilight had one last question to ask. "Princess, you've said that we're your daughters......But you never said if-"
She was cut off as out of nowhere, a sky-blue flash signaled a teleportation spell.
Princess Luna had been aware of rustling in the bushes, but she had thought they were merely rabbits or squirrels. She was proven wrong when she noticed the sky-blue flash of a teleportation spell. The problem was that the flash receded inside the barrier.
She turned to the three other alicorns and said in a grave voice, "It seems that the secret is out."
DUN DUN DUNNNNNNN!!
Anywho, in the next chapter, I will add another character tag.
Probably gonna add an AU tag if season 5 proves me wrong in the adventure part 
*sighs*
I know this chapter isn't my best work, but in my defense, these things aren't pre-written or anything like that and today was rough for me (not going into detail *shudder*)
Edit: I have used some of my precious time to rewrite this, so if you can, please tell me how much better I did this time than with the previous one.
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That went way too smoothly. Things like this don't just get solved in a matter of 30 seconds. Also, Twilight and Sunset believed this way too fast, but that's just me.
6481290
Eh.....I knew someone would eventually.
My subconscious mostly writes these and it wants to get to the 'adventure scenes' (darn you, subconscious)
so yeah....
Wow sneaking into a private meeting is normally a bad idea but if you find out something like this you would think they would have enough common sense to keep your trap shut. Who ever this was, my bet is a spoiled prince, they just got on the bad side of possibly 6 ponies 5 of which are Princesses.
6481351
You'll see soon enough!
Hmm...
I think I know who the flash is!!
Starlight Glimmer anypony?
6481527
Maybe so, maybe not!
Subtle?
...I really hate you.
6481626
Who.....lil' ol' me?
6481618
That right there. That confirmed it.
6481638
6481631
well...not really YOU, more of STUPID CLIFF HANGERS
I can't wait to read more.
Celestia's reason was as horrible as I expected, which added to the fact both Twilight and Sunset were too quick to forgive Celestia make the chapter the worst one so far.
6483008
Meh....
Got nothing against you for saying that.
It didn't help that my cousin was screaming and begging for me to play with him so it was rather rushed and not well thought out.
Add that to the fact that I'm really trying to get to the adventure parts, so yeah......need I say more?
6481290 have to agree here. and that is a poor excuse to send them away. as her students the threat remains. Story had promise but now I go.
6483032
That you'll give more thought on why characters do what they do and will take care of make the charater's actions in-character from now on, not only on this fic.
For another example, Luna: I can't really get her opinion in all of this. How long has she known? Why she didn't react at Twilight Sparkle being her niece or at Sunset Shimmer being a niece she has never met before?
*sigh* I'm too tired to keep bothering myself with this story. This fic was a dud, but keep writing more and we may meet again.
PD: If you haven't realized, the reason so many people were asking for a continuation was because you proposed an interesting premise: Celestia being Twilight and Sunset's mother (and I guess Starlight's too)
For those of you who don't know and have read the first version of chapter 5, I have mostly rewritten it.
So read the revised version now and choose to keep or change your opinion on my story.
Thank you.
6483096
But, not nearly as badly as it would've had she claimed them from the start. As her students, they were more than likely learning defensive magic from her in the first year of being her students. As her daughters, they would've been helpless infants with no control over their magic for at least 3-5 years, depending on their rates of maturity, and even when they gained a little bit of control over their magic, they still wouldn't have had the mana reserves necessary to cast the more powerful spells, which would probably take another 3-4 years to build up at least. At any point during all of this, they could easily have a magical mishap, and cause something to happen that alerts others to their existence.
6486266 doesn't change the fact they are still under threat as students. Heck Rights of Ascension makes that clear that there was even assasination attempts on Student Twilight. Any being connected to the Princess is under threat no matter what.
6486288
6486266
Could you two have a private debate about my story somewhere else?
6486288
The key word there being attempt. If she had been a filly around the age of 2, it would've been successful, and then Celestia, in a grief stricken state, would've went Solar Empress on the entirety of Equus.
6486293
No. No I cannot. Thank you very much for the fine offer, though. I appreciate it. It means a lot to me. It truly does.
6486411
Y'now...just forgot about it.
6486411 out of respect for the author my final words.
I have seen better reason for Celestia not raising Twilight then here but that wasn't the final reason I left this story. It felt to quick on their acceptence that she did the right thing.
This story had a great premise and I wanted to see where it went. I hope that the writers future stories may hit that spot for me.
I say what I say not to be cruel at all but to help. I thought this could have been better and have more struggle with the key fact of Twilight's and Sunset's relation to each other and their mother.
Still a good story, even if it might need to be reworked a bit. Speaking of "reworking", here is a small error I found:
Me think you forgot a word between don't and she.