Think of it like an experiment
Saying that was something Naudia thought in retrospect, a whole two minutes later, probably was a mistake. While it did get Twilight's mind off the subject, ironically by getting her mind on the subject, Naudia didn't like teleporting, she didn't like some of the fumes in Twilight and Starlight's lab, and Twilight tended to leave her behind(unintentionally) any time she researched magic very quickly.
Twilight instantly turned this experiment around for Naudia the moment she turned back from her dictation spell. With a kiss.
They spent a time in that delicious slice of happiness before Naudia realized something and broke it off.
"I think we need to be trying to relax you for this Twilight."
"I know, but coming down to the lab I had to start with that," Twilight said with warmth in her eyes. "Thank you, I don't know what I'd be doing right now without you."
What followed was the most surreal experiment Naudia had ever been a part of. It involved cuddling with Twilight inside of an empty inflatable kiddie pool.
"Are you holding up all right Twi?" Naudia asked.
"I don't know." Twilight felt tense in Naudia's hooves. "It's scary, I'm used to not knowing things, That's why I study. But here… It's me, I'm studying myself, looking in the mirror to find out why I'm not the mare I thought I was."
Twilight let out a laugh that was not at all reassuring.
"Why I'm not…" Twilight tensed up around Naudia, any previous softness gone as her limbs were like iron. "Why I'm not… a pony."
"You will always be Twilight Sparkle, my Twilight Sparkle." Naudia said, "And always remember the results of Park Quantum No-cloning theorem, it's impossible to make a perfect clone of an arbitrary set of states. That's why the mirror pool clones you told me about were different. And trust me if there was somebody who would have noticed you had been replaced it would be me."
Naudia began to stroke Twilight's mane again, and Twilight felt less tense than before, emotionally and physically. After a minute or two Naudia decided to try something, she began to gently massage Twilight's back.
Gradually Naudia could feel Twilight's back soften as she fully relaxed.
"Now," Naudia whispered into Twilight's ear. "don't panic, focus on this feeling, try and remember it, see if you can find a… muscle or a feeling."
Abruptly Twilight flops downward and splats into the kiddie pool.
It is indeed a fortunate thing that Naudia can read emotions like she could because a puddle of purple goop has no face nor voice to express panic. Naudia can feel Twilight start to tense up but not reform herself.
"Whatever you're holding onto, let go of it, it should be fine!" Naudia shouted at the puddle as if Twilight might suddenly become hard of hearing.
Naudia could fell the stress Twilight was going through for far too long before the puddle that was Twilight began to move again. Naudia had trouble trying to figure out how to think about the puddle as Twilight as she sloshed about in the kiddie pool unaided.
Then the puddle of slime coalesced on one side of the kiddie pool and slowly Twilight's head arose from it eyes closed in deep concentration. She opens her eyes and smiles up at Naudia.
"I did it!" Twilight shouts, prematurely.
"I'd love to know how you can talk like that." Naudia says as she watches Twilight's head look down at herself as a puddle of slime.
"We don't have to wonder!" Twilight perked up. "I know how we might be able to find out! Go get my ultrasound!"
"Why do you have an Ultrasound Twilight?" Naudia asked.
Twilight still a head sticking out of a puddle blushed beet red.
"To study future changeling-pony hybrid development."
"Oh."
Twilight had a long moment to herself as Naudia went and got the ultrasound. Staring down at the amorphous blob that was her body, it started to get to her a bit. There was nothing in Equestria or the lands beyond that could explain what was currently happening to her. That was the worrying thing, Equestrian scientists had long concluded that life outside of Equestria was impossible because all stars emitted in infrared, dim, huge red giants scattered randomly from here to infinity in every direction.
So where had that thing come from, what cold dead place did it claw it's way out of? And why was something so monstrous here in Equestria and interested in her? It had to have been that thing that did this, but that answered nothing for her.
"Okay start talking and we'll see what we can see." Naudia said as she put the ultrasound up to Twilight.
"I was going to start talking about it once things calmed down…" Twilight left it there, both her and Naudia knew things had never really calmed down.
"You could just say that you wanted kids Twilight." Naudia said. "We have a lot in common between us but we don't need to examine it all through science or a book."
"Well no, of course not." Twilight said back. "We go on normal dates… not as often as science dates or reading snuggle time, but we would be having the first changeling pony hybrid and we will need to make sure our child will be healthy."
"Before this," Naudia said ultrasound still pressed against Twilight's face who grimaced. "I would actually have little doubt about that, changelings were designed to coexist with ponies in the first place."
It took a moment, but then they realized that nobody was looking at the screen for the ultrasound.
Both ponies turned to look at the ultrasound screen only to find it basically dark, like they were ultrasounding a brick wall and not Twilight's left cheek.
"Lets try somewhere else." Naudia said preparing to get more ultrasound gel.
"That isn't going to work, your body is too dense and strong for an ultrasound." Came a voice from behind them.
Naudia and Twilight looked at the doorway, but only Twilight saw that shimmering figure from earlier. Once again so fast that Naudia could feel the air displaced by the transformation Twilight was in pony form and Naudia heard and uncharacteristic snarl that by rights could not have come from a pony's vocal chords.
But the snarl did match the oddly proportioned purple wolf standing beside Naudia now. It's legs were too long, so long that it put the wolf's height above Naudia's now fully grown changeling queen stature. It's fur was lavender with darker purple accents and a pink streak but there was no hint of a cutie mark, and the wolf's fur was a good deal longer and more voluminous than Twilight's. Without a shadow of a doubt this was Twilight, but transformed into some kind of tall fox-wolf.
"What?" The situation was too surreal for Naudia to fully comprehend and her conscious mind flicked off like a lightswitch.
It was the shimmering figure that broke the silence.
"I'm here to call to confirm with you Twilight." The shimmering figure spoke with a mare's voice, and shimmered into full visibility.
It wasn't that… thing that haunted Twilight and Naudia's nights for the past year, it was something else, the figure in front of Twilight was what she could only call a neon blue wolf-like humanoid made up of glowing light.
Or, Twilight thought looking closer, some kind of force field shell that resembled a wolf humanoid wrapped around something else.
The force field itself was very detailed and as it was being examined closely the creature let it's fur blow in the wind even though they were inside. The creature was massively digitigrade and proportioned very deliberately with curves in Twilight's opinion.
"And who are you?" Naudia asked already settled into a fighting stance.
"I'm Gwynn Hall, here to represent the First Administrator," Twilight noted the capital letters Gwynn put around those two words. "I'm calling in to confirm with Twilight, well be taking a rat over to a gourd and on up to Zaohm." At this Gwynn pointed directly upwards.
"What?" Naudia said and, strangely enough so did Twilight whose hackles had lowered a bit.
"I've come to take you somewhere where you can get an explanation for all this, and to deliver a message." The glowing neon wolf said, pulling out a piece of paper from inside it's fur, Twilight could have sworn she saw a shadow from the other side of it's fur hand the paper outwards.
The neon wolf unfolded the piece of paper and read aloud the short sentence written on it.
"Little black flecks, swirling around, in a dark beady drop at the end of a syringe."
Naudia instantly turned to Twilight who before Naudia's very eyes shifted back into being a pony, all the extra hair length and wolf-like features receding into Twilight's again. Naudia could practically feel the chill that ran down Twilight's spine from the emotional impact alone.
"What does that mean?" Naudia asked her.
"That's from the nightmare I've been having for the last year." Twilight shuddered. "Like it was plucked directly out of my head. No, like somebody plucked the description I… I would have given it, out of my head."
Twilight turned to Naudia, her expression said everything and they silently agreed to follow the wolf monster to meet this "first administrator". Throughout the entire trip through the castle neither of them could forget that they were following a glowing neon blue werewolf thing of unknown origin.
The first thing that greeted them outside Twilight's castle was a rat head of unusual size. It was huge, at least as big as a normal pony's torso.
"Hup hup! Frankie, return trip to the Gourds! Come on now." Gwynn said at the rat head.
The rat head sprang to life and a large patch of pavement suddenly uncloaked itself to reveal the rat head's large flat body, like a giant furry rug. The strangest thing was despite being longer and wider than a carriage the huge flat rat gave off the impression of an excitable pet dog as it attempted to rub it's head up against Gwynn. like a well socialized pet dog Naudia noted as it didn't show any signs of hostility to strangers like her or Twilight.
"All right, hop up." Gwynn said.
"We're riding that giant rat?" Twilight said.
"Yep, should be a short flight over to the gourds on Frankie here." Gwynn said patting the flat rat's shoulder.
"What?" Was all Twilight and Naudia could muster.