The bet

It had been a month since Starlight Glimmer had attempted to destroy the future of Equestria, and Twilight was glad it was over. But she needed to talk to her mentor, Celestia, about her so-called guards. They had dropped the ball again. The train she was taking to Canterlot took seemingly forever to get there. Once it arrived, however, the purple Alicorn quickly made her way to Canterlot castle and into the throne room. Once the doors were shut and the guards gone, Twilight began to speak.
“Celestia. . . it has come to my attention that there is a major problem with the castle guards,” she started.

“And what problem would that be?” asked Celestia, raising an eyebrow.

“Where do I start? Let's see. . . we had the changeling incident where the guards not only failed to protect you when Chrysalis attacked, but also fled from the very enemies they were meant to fight. Then we had the wonderbolts fiasco, where Rainbow Dash was charged with a crime she didn't commit, because your guards didn't notice that someone snuck in where the wonderbolts were sleeping, even though they were supposed to be heavily guarded. What if it was an assassin instead of Wind Rider? Do you realize how easy it would have been for someone to kill them? On top of that, both me, Pinkie and Spike all snuck into Star Swirl “the bearded wing” to steal a time travel spell. Right under the noses of your guards. I didn't even use magic to cloak us; we just hid behind the curtains whenever a guard drew near. Starlight Glimmer also managed to sneak into Star Swirl “the bearded wing.” Either of us could have stolen spells that were a lot more dangerous, such as Festus’ spell, which will turn a pony inside out. Or worse, the spell used for executions. You know the one that causes complete cellular disintegration? Your guards are so bad at what they do that I'm willing to make a bet. I bet that I could sneak into the castle at night, kill you, and steal your crown, shoes and collar right under the nose of your guards and escape unnoticed. And I bet I could do it with a month's preparation and knowledge a common pony would know, as well as basic spells that a normal unicorn could use. If I win, we equip your guards better, as well as re-train them to keep a sharper lookout and be better fighters. If I'm caught, you can decide what happens to me,” Twilight finished, out of breath.

“Alright then. . . you have a bet. But if you fail, you'll become a hermaphrodite for two weeks, understand? Oh and why not a clone of me instead?” the white Alicorn said, giggling.
Twilight gulped. She knew what that meant, but nodded and said, “O-of course. That's what I meant. And not a word to the guards of what's going to happen, got it?”

“Of course! I wouldn't dream of it. Our little bet begins tomorrow morning, alright? And good luck,” Celestia added.
The first thing Twilight did once she left the castle was a transfiguration spell to make her look and sound different. Then she headed to the shady part of town in search of a piece of queen chrysalis’ throne, as it made any magic other than changeling magic impossible. After searching for nearly the whole day, she finally found and purchased a chunk of it, which she made into a horn ring.
She then spent the next few days in Canterlot sneaking onto the castle grounds at night and watching the guards. Especially on how they patrolled around Celestia’s room. She easily found several blind spots. Twilight thought to herself, this is going to be easier than I thought!
Two weeks later, she was ready. The clone was put in place. That night, she made her move. Swiftly sneaking into Canterlot castle and dodging guards just like she had when she snuck into Star Swirl “the bearded wing.” Hiding behind the curtains when they got close, Twilight eventually made her way to her mentor’s room. Noticing two guards protecting the entrance of Celestia’s room, she pulled the same trick that Wind Rider used: tempting the guards with chocolate cake. Sure enough, just like last time, they fell for it, leaving their posts to eat the cake.
Twilight checked to see if the doors to Celestia's room were alarmed. Surprisingly, they weren't. Quickly slipping inside, she made her way to the white Alicorn’s bed. Looking over the snoring Alicorn, she gently slipped the ring over Celestia's horn before casting a full body paralysis spell on her. Then she ransacked the room, eventually finding her crown, collar and shoes.
Placing them into her saddle bags, Twilight decided to have some fun and vivisect her mentor. After all, she had always kind of wanted to. The first thing she did was use some rope she had found, and suspend Celestia by her forelegs from the rafters. She summoned a scalpel and surgically removed her wings at the base, before dropping them onto the floor. Next, Twilight gutted her mentor, removing her organs one by one except for her heart and lungs. She decorated the room with them and wrote a special note in Celestia's blood on the floor. After that was done, Twilight summoned up a hacksaw and cut off Celestia's horn at the base, drinking the liquid magic that oozed from it, feeling her mentor's power seeping into her body as it mingled with her own, before placing it in her saddle bags. She then began to skin Celestia’s body, watching the muscles twitch as she peeled the skin away, leaving the neck and head alone.
Once that was done, she looked her mentor in the eyes and tore her heart out via magic, (noticing an abnormal amount of built up fat on the heart, though that was to be expected due to Celestia's weakness for cake), watching the light fade from her eyes. Then she dried the white Alicorn's pelt using a special spell, before folding it up and placing it into her saddle bag, making her way to the balcony before using a spell to sanitize the room making sure that there was no evidence that she was ever there. She watched the guards patrol, waiting for just the right time to make her escape. Finally, there was an opening and she took it, escaping right under their noses.
The next day, a local unicorn detective named Rebecca Stronghoof met with Celestia outside her bedchambers. Both door guards had been sent off so the two were alone. Celestia expected to find a corpse but was flabbergasted to see just what was inside the room. Rebecca went green once she saw the state of the room, and after a moment, Celestia finally broke the silence.
“I knew someone wanted to take my life, but this…” she trailed off.
The detective as well as Celestia took a deep breath to steady their nerves and stepped into the room.

“Sic semper tyrannis?” the detective asked, seeing the words written in blood.

“It means thus onto tyrants in Latin. Obviously the one who did this doesn't like the way I rule the country,” Celestia replied

“You think?” Rebecca asked sarcastically. "Anyways, this is probably a stupid question, but do you have any enemies?"

“Of course. I rule most of the country under the flag of the solar empire after all; there's always some creature wanting to take over. If it isn't chrysalis trying to take over, then it's a radical from my sister's “New Lunar Republic” wanting to get rid of me for banishing my sister,” Celestia said, letting out a sigh.

“You didn't have a choice though!” Rebecca protested.

“True… and most of the new lunar Republic have accepted that fact. Unfortunately there will always be radicals who think I'm a horrible pony for banishing her, as crazy as it seems.”
Rebecca continued carefully looking over the room, inspecting everything closely. After an hour and a half, she completed her investigation, telling the white Alicorn, “What we have is a unicorn mare—around 18 - 20 years old—who knows how to butcher a pony the same way the Griffins do. Unfortunately, that's all I can tell you until I speak to the door guards as well as the ones patrolling the courtyard.”

“Why do you say it's a unicorn mare and how could you possibly know their age, if I may ask?” Celestia inquired.

“Simple. I found a hoofprint on the balcony railing far too small to be from a stallion. As for the perpetrator being a unicorn, the message written in blood is too perfectly made to have been by hoof. For their age, I studied hoof size and age relations in college," Rebecca explained.
“I see. Let me take you to talk to the door guards first,” the white Alicorn said.
Rebecca nodded. Unfortunately, the two door guards didn't see who was nice enough to give them cake, but they did say it was around midnight when it showed up. And as for the guards patrolling the courtyard, they hadn't seen anything unusual at all that night. After two weeks the case went cold. Rebecca did find out about the bought piece of chrysalis’s throne that was purchased by an unknown pony who was heard saying it was going to be made into a horn ring, which explained why there wasn't much of a fight. Other than what she found in Celestia’s bedchambers, nothing turned up and Celestia finally admitted defeat.
Twilight gave back her mentor's shoes, crown, and collar, but kept her snow white pelt, having a nice pair of bedroom curtains made from it, as well as several throw pillows.
As for the castle guards, with Applejack as their teacher, they were taught how to quickly, effectively, and non-lethally take down a target, as well as be more observant of their surroundings.
Twilight did try and sneak into the castle after dark several different times as a pop quiz of sorts, and each time she was successfully apprehended, which made her quite happy knowing the guards were doing well and remembering their training.
After several months, Twilight was content in knowing that at least for now, Star Swirl “the bearded wing,” as well as Celestia, were protected.