It's been two months since the crystal empire incident and we now find Sonic and Twilight making their way through ponyville.
As they walked, Sonic noticed that Twilight was happily humming what sounded like her Singing.
"You seem to be in a good mood this morning, Twilight." Sonic commented.
"That's because I have a feeling today is going to be absolutely perfect!" Twilight chirped.
"In what way would that be?" Sonic asked.
"I'm not completely sure, but I'm just certain that it will." Twilight responded.
"Well, as long as you're not stressing over something, I guess it's a good way to start." Sonic said.
About a second after Sonic said that, the duo became completely soaked when rainwater suddenly fell.
"That was not funny Rainbow Dash." Sonic said as he and Twilight shook the water off.
"Terribly sorry, darlings. I'm afraid I'm... I'm not good with the thundery ones." Said a voice that definitely didn't belong to Rainbow Dash.
When the duo turned towards it's source, they were surprised to see Rarity using her magic to control the clouds.
"Rarity, what are you doing?" Twilight asked.
"And what happened to your cutie mark?" Sonic asked as he and Twilight saw that Rarity had Rainbow Dash's cutie mark instead of her own.
"Whatever do you mean?" Rarity asked as she somehow made it both rain and snow at the same time, "I'm simply doing what I've done since the day it first appeared. Does my sky look fabulous or what?"
Not too long after she said that, the trio heard several ponies complain about the weather.
"I think its best if I take it from here Rarity." Sonic said before turning into his super form and began to push all the clouds away.
As the day progressed, Sonic and Twilight saw that Rarity wasn't the only one of the six who had been acting weird and had their cutie mark swapped.
The duo also saw Rainbow Dash with Fluttershy's cutie mark at Fluttershy's cottage trying to care for the animals but wasn't having much luck until Sonic calmed all the animals down.
After that, they found Fluttershy with Pinkie's cutie mark at Sugar Cube Corner trying to make customers laugh. Pinkie had Applejack's cutie mark and was working at Sweet Apple Acers, and Applejack with Rarity's cutie mark was at the Carousel Boutique trying to make dresses but like the others before them, they weren't having too much luck doing so.
"I swear, if Discord wasn't reformed now, I would somehow find a way to pin all of this on him even though he would of been encased in stone at the time." Sonic said as he and Twilight finished explaining everything to Spike.
"That kinda does sound like something Discord would do." Spike admitted before asking, "Anyway, any ideas about how this happened?"
"I think I know what happened." Twilight spoke up.
"What is it?" Sonic asked.
"Well, do you remember how yesterday I got a special delivery from Princess Celestia that was a book." Twilight asked.
"Yeah." Sonic responded.
"Well, in the letter that came with it, the princess said the very last page was Stars Swirl the Bearded's secret unfinished masterpiece and that she hoped that I can understand and rewrite it." Twilight explained, "I casted the spell so I could find out what it was, but nothing seemed to happen."
Twilight then walks over to a nearby display case that held the Elements of Harmony.
"But now I know something did happen. The spell has changed the Elements of Harmony!" Twilight exclaimed as she, Sonic, and Spike saw that all of the elements (except for the element of magic) had swapped colors with each other, "That must be why their cutie marks are all wrong!"
"So just cast a counter-spell to switch them back." Spike simply said.
"I would, but there isn't a counter spell!" Twilight said.
"How about the memory spell?" Spike suggested.
"It's not their memories, Spike. It's their true selves that have been altered!" Twilight explained.
"I may not be an expert in magic like you are Twilight, but I have a feeling Zecora's cure for the cutie pox won't work either." Sonic said, "If only we can remind them what their true purpose really is. It really pains me to see our friends like this."
"That would make everything easy." Twilight said before suddenly getting an idea, "Our friends..."
"What is it Twilight?" Sonic asked.
"I've got it! I know what to do!" Twilight exclaimed happily.
"Really? What is it?!" Sonic asked.
"I'll explain on the way, but for now, let's get going!" Twilight exclaimed before grabbed the Elements of Harmony and ran out the door.
"Hey! Wait up!" Sonic exclaimed as he and Spike gave chase.
Not too long later the trio are making their way through ponyville before spotting Fluttershy who was about to climb into a hot air balloon.
"Fluttershy! Wait!" Twilight called out.
"Oh, hey Twilight, Sonic, Spike." Fluttershy said as she turned towards the trio.
"Where are you going?" Sonic asked.
"I'm moving back to Cloudsdale." Fluttershy explained, "I don't know what's wrong, but I can't seem to make anypony laugh."
"Before you go, I was wondering if you might be willing to help Rainbow Dash." Twilight said, "She's really struggling with her animals.
"But, I don't really know anything about animals." Fluttershy said.
"But you do know something about Rainbow Dash." Twilight countered.
"I... know that she's a true friend, and I'll do anything I can to help her." Fluttershy said.
"Great! I'll get us there in a flash." Sonic said before using chaos control to teleport himself and the group to Fluttershy's cottage.
When they arrived they were shocked to see Rainbow Dash tied up in a cooking pot as the animals danced around her.
"Oh no!" Fluttershy exclaimed, "Twilight, Sonic do something!"
"Sorry Fluttershy, only you can help Rainbow Dash." Sonic said, "She needs you, Fluttershy."
Although Fluttershy seemed nervous, she nodded before walking up to the animals.
Um... Hello? Little... woodland creatures? I know that you're all very upset and feel like giving Rainbow Dash a hard time, but we'd all really appreciate it if you'd calm down and, um, maybe... rest for a bit?" Fluttershy said as the animals stopped what they were doing and started to gather around her.
"Oh! Uh... look! Here's some nice, juicy leaves for you to munch on." Fluttershy said as she grabbed a bowl of food and presented it to the animals, "And some crunchy, munchy acorns too. Uh, wouldn't you like to take a break and have a little snack?"
After handing food around, the animals had finally calmed down and began to eat.
"Aww, look at that. I guess you were all just cranky because you were hungry. Oh, you are very welcome, little friends." Fluttershy said before being pulled into a hug by a bear.
"Goodness, it's like I can understand them!" Fluttershy said as a pink aura formed around herself, "I... I feel strange, like... like this is what I'm meant to do, like this is who I am! My destiny!"
As soon as Fluttershy said that, Twilight grabbed the element of kindness before placing it on Fluttershy's neck, causing a bright flash.
When the flash died down, Sonic, Twilight, and Spike saw that Fluttershy had her cutie mark back.
"Wha... what happened?" Fluttershy asked as she looked around.
"It's a long story, but we'll tell you later." Sonic said.
"Um, hello? Friend trapped inside, remember?" Rainbow Dash spoke up.
"Don't worry Rainbow, we didn't forget about you." Sonic said said as he went to untie Rainbow Dash.
After repeating the process four more times, all of the mane six where now restored to their normal selves.
After a small celebration, Twilight claims that she knows how to complete Star Swirl's spell, causing the group to hurry back to the library.
"Are you sure you got this Twilight?" Sonic asked, "I don't want you to end up accidentally hurting yourself.
"I'm positive Sonic." Twilight responded as she grabbed both the spell, and a quill, "I've never felt so sure in my life!"
"If you say so, but just to be safe, I'm going to be continually giving you energy from the chaos emeralds in case the spell requires more magic than you can produce." Sonic said as he took out a chaos emerald.
"You go ahead and do that, I'll focus on finishing the spell." Twilight said.
With that said, Sonic placed a hand on Twilight's back and shortly afterward, a green aura began to form on Sonic's arm before spreading onto Twilight.
Once Twilight felt the additional energy flowing through her body, she began to write the spell.
From all of us together, together we're friends. With the marks of our destinies made one, there is magic without end!
As soon as Twilight finished and placed the book down, her element of magic began to glow before suddenly creating a wave of magic throughout the library.
Before Sonic could remove his hand from Twilight's back, the other five elements shot a beam at the duo, creating a white barrier around them.
This continued for a moment before a bright flash flooded the entire library.
When the flash died down, Spike and the remaining five saw two scorch marks on the ground. One in the shape of Twilight's cutie mark where Twilight stood, and one in the shape of Sonic's symbol where Sonic stood.
"Where did they go?" Fluttershy asked, causing everyone have worried looks on their faces.
In what appeared to be an ethereal space full of stars and nebulae, we see Sonic and Twilight as they looked around with confused expressions on their faces.
"What is this place?" Sonic asked aloud.
"Hello? Is anypony there? Where are we?" Twilight called out into the stars.
"Congratulations, Twilight. I knew you could do it." They heard a voice call out.
When the duo turned to see who it was, they saw that Princess Celestia was walking towards them.
"Princess... I don't understand. What did I do?" Twilight asked.
"You and Sonic did something today that's never been done before. Something even a great unicorn like Star Swirl the Bearded was not able to do, because he did not understand friendship like the both you could." Princess Celestia explained, "The lessons you've learned here in Ponyville have taught you well. You have proven that you're ready, Twilight."
"Ready? Ready for what?" Twilight asked.
"And if you don't mind me asking, why am I here?" Sonic asked.
"Sonic, you where always there to support Twilight when she needed it." Princess Celestia explained, "Never once did you turn your back on her, or her friends. You where always willing to help anyone in need, and because of that, you are ready for even more responsibilities as prince."
"What do you mean?" Sonic asked.
As a response, Princess Celestia began to sing.
You've come such a long, long way
And I've watched you from that very first day
To see how you might grow
To see what you might do
To see what you've been through
And all the ways you've made me proud of you
It's time now for a new change to come
You've grown up and your new life has begun
To go where you will go
To see what you will see
To find what you will be
For it's time for you to fulfill your destiny.
As Princess Celestia finished, Sonic and Twilight's chests began to glow before a blob of magenta and blue came out.
The blobs then begins to circle around the duo, causing them to float upward.
This continued for a few seconds before a bright flash engulfed the entire space.
High above ponyville, two flashes suddenly appeared, one taking the shape of Twilight's cutie mark, while the other took the shape of Sonic's symbol.
The two lights then begin to descend to the town, landing in front of where Spike and the rest of the mane six where.
The lights flashed once more before finally dying down, allowing the group to see two figures, that they recognized as Sonic and Twilight.
But upon a closer look, they group saw that the duo had changed.
Twilight had appeared practically the same but she now had two wings on her back.
As for Sonic, his quills now appeared to be sharper than they used to. He also grew more quills on his wrists, ankles, upper legs, and in the ends of his muzzle. His shoes and gloves have changed as well as his gloves seemed more "bulky" with gray bands on his wrists, while his shoes appeared to be sleeker while the bottom was now made of metal.
"Sonic? Twilight? Is that you?" Applejack asked as she and the others walked up to the duo.
"Cool! Twilight's got wings now! Awesome! A new flying buddy!" Rainbow Dash exclaimed happily, "And Sonic now looks 20% cooler now!"
"Why, Twilight has become an Alicorn." Rarity said, "I didn't even know that was possible."
"Yay! Alicorn and cooler Sonic party!" Pinkie exclaimed.
"Wow Twilight, you look just like a princess!" Fluttershy said.
"That's because she is a princess." Princess Celestia said as she appeared in front of the group.
"Huh!?!" The group gasped as they turned towards the princess.
"Hold on a second!" Pinkie exclaimed as she grabbed a glass of water from out of nowhere before taking a sip, only to spit it out in a surprised fashion.
"A... A princess?" Twilight asked, absolutely shocked.
"Since the day you came to Ponyville, you've displayed the charity, compassion, devotion, integrity, optimism, and of course, the leadership of a true princess." Princess Celestia explained.
"But... does this mean I won't be your student anymore?" Twilight asked.
"Not in the same way as before." Princess Celestia responded before adding, "I'll still be here to help and guide you, but we're all your students now, too. You are an inspiration to us all, Twilight."
"But... what do I do now?" Twilight asked, "Is there a book about being a princess I should read?"
Princess Celestia giggled, "There will be time for all of that later."
The very next day, a princess coronation ceremony was held in canterlot where Twilight was presented as the newest princess of equestria.
After saying how important friendship is and saying how she'll do her best to support equestria the best she could, we now find Twilight, the princesses, Sonic, Shining Armor, Spike, and the rest of the mane six in the throne room where everyone was congratulating her.
"Who would of thought, my mom's star pupil becoming a princess?" Sonic asked as he had an arm wrapped around Twilight.
"I'll say that I didn't see it, but am happy that it did." Shining Armor replied as he tried to hold back his tears of joy.
"As happy as I am too, I'm still a little uncertain about this." Twilight said.
"Twilight, I know you're worried and all, but you have nothing to stress about." Sonic said he took him arm off her.
"Why's that?" Twilight asked.
"Because you me and the girls." Sonic responded, "Sure, being royalty can be tough at times, but with some guidance, you'll be ready in no time. You'll even have me, mom, aunt Luna, and Cadence to help you out along the way.
"I know that, but what if I mess up?" Twilight asked.
"You're not going to mess up Twilight, I'll make sure of it." Sonic assured her.
After taking those words in for a moment, Twilight smiled before saying, "Thanks Sonic."
"Hey I'll always be there for you Twilight." Sonic said before hugging her, "And I'd be a bad brother if I wasn't."
Twilight was shocked for a moment, but she then smiled before returning the embrace.
"Who wants cake?" Pinkie called as she came in with a large cake.
"Come on, let's get some cake before my mom decides to hoard it all to herself." Sonic said as he and Twilight ended the embrace.
Chuckling, Twilight nodded before she and Sonic made their way towards the cake.