The First Clue/Finding the Second
The five mares finished the meal at lightning speed, even Fluttershy, and they zipped towards the library through the dark night. All of them were out of breath as they arrived, and Rainbow Dash was the only one with the strength to knock. They all stood with abated breath until the door slowly opened, thanks to a small purple dragon. He could barely speak before being trampled by the others, running towards Twilight.
"I found the clue!" Cheered Rainbow Dash, a burst of adrenaline causing her to speak faster than Pinkie on a good day.
"Well then, let's hear it," said Twilight with a smile. Rainbow Dash struggled with the plastic wrapping until Twilight gently pulled it off, and Rainbow Dash flashed her a grateful grin before reading.
"The colt has a father, as I'm sure you all know,
but to find it, you move awful slow!
I can assure you, in Ponyville they reside,
More specific than that I cannot provide."
"Twilight dear?" Rarity interrupted the short bout of silence that filled the library. "When's the foal due?"
"Glad you asked. Let's see, it's June, and the doctor said the baby was probably conceived about five months ago since I'm just starting to show, and the average gestation period is about ten months... November, or maybe a bit sooner or later. Now, I'm assuming you girls want to review the clues, so just ignore me."
"Thank ya Twilight," sighed Applejack as she collapsed on the ground, followed by Pinkie, Rarity, Rainbow Dash, and finally Fluttershy.
"Now, so far we know that the father lives in Ponyville," declared Rainbow Dash, seemingly taking charge.
"An' we know one o' us here knows who the father is," added a suspicious Applejack.
"But who would keep a secret like that from us?" Whispered Fluttershy, looking at each of them worriedly.
"Well, when Twilight has the baby, we'll throw her a party!" Pinkie's outburst was ignored by the others as they each stared suspiciously at each other.
"Well either way, we'll find out when we do. Now who wants to get some sleep?" Rainbow Dash fluttered her wings tiredly, accompanied by an overly-loud yawn.
"You can stay here," offered Twilight, "And help me plan!"
"Plan what? The party?" Pinkie was still bouncing around, despite the sleeping blue pegasus next to her, jumping over her back and forth.
"No! What do to when he-or she-is born. I'll be staying here in the library, and the foal will stay with me for a while, but what about when they need their own room? I suppose I could use my old Griffon room, but it'll need cleaning..."
In the morning, the girls were more than glad to make breakfast for Twilight, creating a buffet-sized meal for her. "I can cook, really girls," she sighed, but sat down and began to eat. She was about halfway through the meal when something dawned on her. "Did you read the back of the note?"
"No," came a chorused response, and Twilight smiled.
"Each clue will have a front and back. The front has a clue about the father, the back a clue about where the next clue is. When you're done you can-" She was cut off by a gust of wind and a rainbow blur. Rainbow Dash sat at the table with a grin, ready to read the second clue again. "Or you can read it now," she sighed resignedly.
"Your second clue isn't hard to find,
located somewhere way up high.
A cloud walking spell you may require,
to end up in the home of a high-flier."
Rainbow Dash stared confusedly at the letter, when it dawned on her. "My house?" She asked, staring at Twilight.
"I'm not going to say. But if you want that cloud walking spell..."
"Yes!" Cheered Pinkie, jumping in front of Twilight.
"Alright," sighed Twilight, and closed her eyes, recalling the spell as she cast it on the mares around her. "Now have fun, and be safe!" She realized she was speaking to an empty room, and turned around, magically lifting the dishes. "This is so much more difficult than it should be..."
The five mares had finally made it to Rainbow Dash's home, having been carried up there by Rainbow Dash one-by-one. They sniffed around, searching aimlessly for some sort of rolled up piece of paper. This time, Pinkie was the one to find the message, and much faster than the day before.
"Lookie-lookie-look!" Exclaimed the pink pony, pointing wildly out Dash's bedroom window. The others gathered round, staring out the window, and they all facehoofed simultaneously.
"How could I have missed that?" Muttered Dash under her breath, but Pinkie was too busy bouncing around to hear her.
"You may recall that I never said
that the father was a stallion.
The next clue you can't discover
until you've had time to recover.
The next clue you can take
by looking inside a cake!"
"So the father could be a..."
"Mare." Fluttershy whisper-finished Rarity's sentence as Rarity collapsed to the ground, her eyes closed. Fluttershy gently lifted the unicorn, laying her on Rainbow Dash's shockingly-clean bed.
"Well tha' sure does narrow i' down," said Applejack sarcastically, looking around the room. "Can ya take me home, Dash?" The rainbow maned pegasus nodded, and leaped off the cloud, Applejack securely on her back as they glided towards Sweet Apple Acres.
The other ponies were carried home by Rainbow Dash, and she dragged herself up to her cloud home, collapsing tiredly on the bed with a sniff.
"Really Twi? You bend that way? You shoulda told me that." And she fell tiredly asleep.
Twilight looked up at the cloud message in the sky, and waved her horn, magically vanquishing it. "Red herrings are entertaining," she smiled, and looked over at the sleeping Spike. Standing from her couch and setting her book down, she trotted around, magically extinguishing each candle, then finally the main lights as she cantered up the stairs and into her room.
Flopping down on the bed, she magically summoned her book. Lighting a candle next to her, she opened the book, letting the bookmark fall to the ground as she read "Parenting for a Single Mare".
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this is one of the most confusing stories I've read, it stumps me.
Only one other story has me for a tizzy, but that is because the writing is as if the person is having a mental breakdown.
wait, the dad could be a mare?!?!
how the fuq does that work?!?! I'm on to you Lyra.
Never said it was a stallion or mare or pony for that matter so Spike is a possobility
780647 Magic and ^
780647
MAGIC
But not kidding multiple stories use magic in mare/mare relations to get foals
I'll tell you this much- IF it is a mare, yes it was magic :D
This is one of those stories thats great to find after its finished because then you can just read the whole thing in one go. The waiting is TOOOOOORTURE
. Great story though 
sooo...should I use mr bean here or something?
So basically you've just added everybody to the list
all genders apply, all species apply.
Back to square one
So re-read edit
1 of the others knows under pinkie-promise
May not be a stallion
lives in ponyville
Wait.....Twilight reading "Parenting for a Single Mare"
R63-clone or self-insemination?
There is no good evidence to rule out anything yet!!!!
That's right... EVERYbody to the list. At least you know they live in Ponyville.
780733 Do please.
780844a'ight
magic
i3.kym-cdn.com/entries/icons/original/000/006/453/BEAN.png
Okay... poll time!
How long do you want this to be?
A. Just three clues, then timeskip to the birth.
B. Five clues, then time skip.
C. Seven clues, then time skip.
D. X number of clues, then random fillerness to the birth instead of timeskip.
Y'all have an hour, because I want to finish this!
its Spike calling it.
780861 make this last man, make it last.
As long as it could possibly be with making it seem stretched thin, maybe seven clues. C
I think D.... It's the one with the most torture potential, without limit you can lead us to any conclusion you want us and even then you could throw in a few dream sequences to further muddy the trail.
Even the birthscene, or rather especially the birthscene.
You could have any character's point of view looking at the 'father' and then have the character wake up
Wait..Why am I giving advice to torture the reader? oh yeah, I'd like the story to be drawn out as much as possible so I can see and add to the insane theories.
I don't want you to use a number of clues before you go to the birth, I want you to play with your audience. I want you to simply write a story you feel happy about. If you choose to end it in 3 hints or 3000 hints so be it. but do it because you feel it flows right with the story. Not because the readers want closure, who cares about them?
hmmm, I get the impression that the Red Herring she was referring to was the last sentence, so I'm gonna stick with saying it's a stallion. It could be anyone, so my first guess is Doctor Whooves (If twilight is going to be a single parent, the dad has to have a good reason and being a time traveler might just be good enough). My second guess is Trixie (one night stand of hate sex which led to a magically induced pregnancy)
EDIT: It could be a changeling as well. That's my third and final guess.
D
I'm gonna be crazy and say that SNAILS IS THE FATHER!
It's not a colt-I promise that much. Or a filly. It is an adult/grown pony.
As for the red herring... /winks.
And you know what? I'm just going to keep writing until I think it's time to close this off.
Oh, and by the way, I'm still debating who the father is xD
shufflingdead.com/TotW/ShamefulHuman/M-Night-Shyamalan.jpg hwat a twhist!
OK here's what I got.
Something about a red herring. Pretty sure that symbolizes something, or it has some other meaning from the fish. Remember hearing about it from school, but can't remember the meaning.
Stallion:
One of the Mane 6 knows him.
To me that sounds like a good friend/family type of "know".
So, Big Mac . . . Blueblood? . . . Brayburn . . . Caramel?
Mare:
Needs to be a unicorn. Reason being, if a unicorn could get herself pregnant, . . . Not ending well for society.
So, Trixie . . . Vinyl Scratch? . . . Lyra?
Anybody else have any idea?
Or, Twilight could turn some random mare into a stallion for the night... I'm sure Twilight could pull it off. But I'm not saying what happened specifically.
well, what can i say...
got it
Wait for it
I want more of this!
Sometimes I think Twilight is an ass sometimes.
The father might not be a stallion... because he's not a pony. If so, I called it.
793098 Come on I suggested that spike was the dad last chapter.
get your head in the game.
My other theory is that twilight used magic to reproduce asexually.
I vote D and I call Celstia as the dad trololol
I give you 8/5 moustaches
I find this both entertaining and...well, I thought I was going somewhere with that.
Please continue!
762555 that look more like her mom then twilght