Just because I got a billion and a half requests for an epilogue, here you go. Written pretty much on the spot with little to no thinking at all.

Please, for the love of Celestia, PM any spelling errors to me rather than leaving them in the comments.

Mr. Twilight Sparkle
Epilogue

…

Spring, the time for rebirth, renewal, and when most ponies had their foals.

This spring, there were a grand total of nine new foals being born in Ponyville, five of which were blessed to be born among the strangest family the town had ever seen in their lives.
Twilight Sparkle's secret of being a Prince had 'somehow' leaked out, thanks in no small part to the actions of a small trio of fillies.

The summer wedding had been a private affair in Canterlot, presided over by Princess Celestia. Only direct family members were invited, and let's just say, the family of the Prince was very confused to say the least.
But right now, it was spring, and the resident librarian, Prince Twilight Sparkle, was pacing madly back and forth outside the delivery room.

Pinkie Pie, Applejack, Rarity and Rainbow Dash were also waiting with him, with decidedly much less pacing on their parts.

This left Fluttershy as the one who was as of now giving birth to her foal.

“Remind me why I can’t be in there again.” Twilight asked Spike, who was sitting on his back this whole time.

Spike simply shrugged. “You know Fluttershy. She’s too embarrassed to have anypony in there with her other than Nurse Redheart.”

“Right.” Twilight hung his head. “I hope she’s alright. She looked so afraid when she felt the foal coming.”

Rarity lay on one of the comfortable waiting sofa, a soft, yet bemused smile on her lips. “This is Fluttershy you’re talking about, the little mare who stared down a dragon. She will most certainly be fine.”

Dash chuckled. “You’re more nervous than the rest of us, aren’t you, Husband?”

Twilight looked up at his four wives. “Yea, I guess I am. I mean, I’m going to be a father…” He turned and started slamming his head into the wall, leaving holes in the stone and wood from his horn.

Pinkie Pie giggled cutely. “Oh Twi, you worry wart. All your foals are going to be just perfect.”

“All our foals.” Applejack corrected Pinkie Pie, her fellow wife to the Prince.

Before anypony else could speak, Nurse Redheart stepped out from the delivery room. “Prince Twilight, Princess Fluttershy requests your presence. I can only permit one of you in at a time.” She smiled past the Prince, at Spike specifically.

“I get it, I get it.” Spike huffed and hopped down as Twilight chuckled at him. “You’ll all get to see Fluttershy and the foal soon enough.”

“Oh my.” Rarity’s head perked up. "I do hope the delivery room is ready for another expectant mare… like right now.”

Redheart and Twilight took one look at each other, and rushed to assist the white and royal purple Unicorn.

...

By the end of that day, somehow, all five mares had given birth. The most exhausted pony of all was the Prince.

Fluttershy had blessed them with a sweet little filly. Her coat was a slightly darker yellow than her mothers, and her mane purple with soft pink streaks, and the cutest little wings. Her eyes were a bright green.

From Rarity, a pale lavender coated colt, with midnight blue mane and tail. This little unicorn had her mother’s eyes.

Rainbow Dash was the proud mother of a Pegasus colt as well, with a multi shaded purple mane and tail, the coat being a bright orange, and his eyes being of sparkling amber. Oddly, he looked a lot like Scootaloo.

Applejack mothered a healthy little filly, and much to her surprise, a Pegasus. The little bundle of joy sported a bright red mane and tail, light red coat, and amazing golden eyes.

Finally Pinkie Pie. She gave birth to a pink maned Unicorn filly, with a coat that was a slightly pinker shade of her father’s. Her eyes were a bright emerald green.

Twilight looked over his foals. Three fillies and two colts. His chest swelled with pride.

“What’s their names?” Spike asked as he looked through the window into the maternity ward.

“Meadow Song, that’s Fluttershy’s filly. Rarity and I decided on Midnight Star for the little colt. Rainbow Dash didn’t surprise me when she suggested the name of Shooting Star, and I have to agree, it is a very good name. Applejack was rather shocked that she had a Pegasus, but was adamant on calling her Appleseed.” Twilight then sighed. “And Pinkie Pie… my sweet, sweet Pinkie Pie… She wanted to call our filly Party Popper Sparkle Pie.”

Spike stifled a laugh. “Obviously you didn’t agree, right?”

“It is the perfect name for her.” Twilight laughed softly.

The baby dragon stared in shock at his best friend, boss, big bro. “You’re kidding, right?”

“Not at all. Her name is Party Popper Sparkle Pie.”

Spike just looked dumbfounded, and a moment later, he belched up a letter.

Twilight caught it in his magic. “And… the news I’ve feared all day.”

“Feared? Why?” Spike asked.

“Well… You see…” Twilight sighed. “My wives are not the only ones I got pregnant. There were two others, and even though they had both used protection spells… my seed was even stronger.”

Spike’s eyes went wide. “Wait… You can’t mean…”

“Princess Celestia and Princess Luna.” Twilight sat down on his rump. “They kept this a secret for as long as they could by using illusion spells. But in the end, they couldn’t prevent the inevitable.”

Spike was at a loss for words, and Twilight continued. “I’m being summoned to Canterlot, right now, to meet my other foals. What will all of Equestria think about this?” Twilight turned to Spike. “Please tell my beautiful wives that I had to go to Canterlot at the summons of the Princesses.” With that, and a bright flash from his horn, Twilight Sparkle vanished.

He appeared a moment later in his library home at the School for Gifted Unicorns. From there, he made his way quickly to the palace, and to the Royal quarters of the Princesses. He found the door was being guarded by his brother.

“Uh, hi Shining…” He grinned sheepishly.

“Hey Twilie. You’re supposed to go right on in. They wouldn’t let anypony but Dr. Reeds inside for some reason and asked that I make sure nopony but you go on in.”

“Thanks BBBFF.” Twilight nuzzled his big brother and entered the private chambers, closing and sealing the doors behind him.

Once the doors closed, he felt another wave of magic flow over him, and he could suddenly hear voices.

“Twilight, we’re in here.” Celestia called out.

The Prince walked into the bedroom and stopped in his tracks.

The Solar Princess was feeding a pair of foals.

“T-tw-twins?” He stammered in shock.

“Yes, twins.” Celestia smiled with immeasurable pride and joy.

“Bu-wha-how?”

Celestia laughed, a most wonderful of sounds. “Oh my silly Prince. Only one is mine. The other is Luna’s. She’s incapable of properly feeding, seeing that she didn’t produce any milk.”

“Oh.” Twilight relaxed as he stepped closer to see the pair of tiny winged and horned foals. “They- oh gosh. They’re both Alicorns?” His eyes were impossibly wide at the sight.

“Of course they are. Both their mothers and father are Alicorns. These two are the first naturally born Alicorns, ever.” Celestia nuzzled the golden coated one, followed by the silver coated one.

Luna entered the room from a side door that lead to the wash room. “Ah, Prince Twilight Sparkle, we are so please thou could make it.”

“How could I not come? I mean…” He looked at the pair of foals. “So, what are their names?”

Celestia nuzzled the tiny colt with the golden coat and flaming red mane. He opened his amethyst eyes and looked at Twilight for the first time. “This is Prince Solaris.”

Luna nuzzled the other foal. “And this is your daughter, Princess Selene”

Twilight walked over and smiled at his secret son and daughter. “My wives are going to kill me.”

Luna laughed. “Dear Prince, they shalt do no such thing. They have known for near eleven months, but hath been sworn to secrecy.”

Twilight twitched.

“Twilight?” Celestia looked a little concerned as a slightly crazed grin cracked across Twilight’s lips and his eyes shrunk to pinpoints.

A quick jolt of magic from Luna snapped him out of it. “Ow.”

“Thou were looking less than sane my Prince.” Luna grinned a little. “T’would not bode well to lose you to insanity, not when you have your children to care for.”

“Seven foals… I doubt my job as Ponyville Librarian will be able to pay for them all.”

Celestia stood up as Luna took over cuddling the foals. She walked over to Twilight and affectionately nuzzled him. “You need not worry Twilight. I told you before that, as a Prince, you need not worry about money.”

“I know, I know… but still. I don’t want my foals to grow up spoiled. I’ve met Silver Spoon and Diamond Tiara so I know what an upbringing like that can do to a foal.”

The Princess gave Twilight a reassuring smile. “They shall not be spoiled. All their needs shall be taken care of. Their wants on the other hoof, that is where money will be needed. You can rest assured that all your foals will be well taken care of.”

“Thank you Princess.” Twilight relaxed. He came over to the bed and smiled at Solaris and Selene. “Wow, Alicorn foals. I just hope they don’t blow anything up. Baby Unicorns have been known to have magic surges, and baby Pegasai have been known to have ‘flight’ spurts.”

Celestia and Luna looked at each other. “Did thou knowest this Sister? We most certainly did not.”

Celestia nodded a little. “I knew, but honestly, I had not thought about that.”

All three turned to look at the long ignored Dr. Reeds, the Unicorn doctor who had been present the whole time.

“What are you looking at me for? I’ve never had any foals of my own and I know nothing about Alicorn foals. For all I know, they may not develop their magic and ability to fly for years to come. Or they could blow up half of Canterlot with an uncontrolled magical surge.”

“Ah, the joys of parenthood.” Celestia deadpanned. “Twilight, please, for the sake of Equestria, never get either of us pregnant again.”

“Get who pregnant?” Princess Cadence stood in front of the open doors, a VERY sheepish looking Shining Armor standing behind her.

She then spotted the pair of foals and her eyes lit up in delight. “Shining dear. I think we just found the answer to your impotence.” She smiled as she turned to face Twilight, a seductive look in her eyes.

“Oh for the love of Celestia…” Twilight backed away.

...

The End.

Author's Notes:

For those wondering, Shining isn't actually impotent. He is actually remarkably virile and healthy and more than capable of fathering foals...

It's just that his special talent for protection magic and shielding spells is so strong, that it keeps him from actually being able to get any mare pregnant... The poor guy.