Magical Mystery Cure (Alternate Version)

Summary
After discovering that Twilight accidentally mixed up her friends' cutie marks, Sonic and his friends must find a way to help her restore them to normal, along the way, the Mane Six will ultimately discover their destiny.

Differences

 * Applejack, Fluttershy, Pinkie Pie, Rarity and Rainbow Dash all ascend to alicorn princess status along with Twilight.

Transcript
[One early morning in Equestria, Sonic and Tails were flying above Equestria in the Tornado, chasing Dr. Eggman, Orbot and Cubot in his Egg Mobile. Eggman is carrying a capsule containing animals]

Sonic: Drop the critters, Eggman!

[Eggman presses a button, releasing the capsule as it drops]

Dr. Eggman: [mockingly] If you insist.

Sonic: [gasps]

Tails: [shocked] Whoa, that's harsh!

[Sonic spin dashes off the Tornado, reaching for the capsule's button but misses. Tails catches him on the Tornado]

Tails: We'll have to swing back around for it!

Dr. Eggman: Predictable.

Orbot: Very.

Cubot: He must really love those things!

[Eggman shoves Orbot and Cubot away and pulls out a laser gun. He aims it at Sonic and Tails, then shoots at them. The laser hits the Tornado's wing]

Sonic: We're hit! Uh-oh!

Tails: Hold on!

Sonic: [looks from below] Hey, isn't that Ponyville?

Tails: Yeah, it is, the landing pad for it should be just up ahead!

Sonic: Less LOOKING, more LANDING!

Tails: Alright, I can land this, but it's gonna be bumpy!

[Sonic and Tails drift off towards Ponyville]

[Meanwhile, Twilight Sparkle had just woken up to a new day in Ponyville]

[Twilight Sparkle]

Morning in Ponyville shimmers

Morning in Ponyville shines

And I know for absolute certain

That everything is certainly fine

There's the Mayor en route to her office

There's the sofa clerk selling some quills

Davenport: Morning, kid!

[Twilight Sparkle]

My Ponyville is so gentle and still

Can things ever go wrong?

I don't think that they will

Morning in Ponyville shimmers

Morning in Ponyville shines

And I know for absolute certain

That everything is certainly—

[splash]

Twilight Sparkle: Rainbow Dash, that's not funny!

Rarity: Terribly sorry, darling. I'm afraid I'm... I'm not good with the thundery ones.

Twilight Sparkle: [gasp] Something tells me everything is not going to be fine.

Twilight Sparkle: This is bad. This is very, very bad.

Sonic: Like, how bad are we talking about here?

Spike: What's going on? Why is this happening?!

Knuckles: Yeah, there's got to be a explanation!

Dr. Eggman: I'm kinda clueless on what's going on here.

Twilight Sparkle: [realizes] Wait a minute, that's it! Last night, I got a special delivery from the princess.

[Flashback]

Twilight Sparkle: Dear Twilight Sparkle,

The spell contained on the last page of this book is Star Swirl the Bearded's secret unfinished masterpiece. [gasps] Ooh! ''He was never able to get it right, and thus abandoned it. I believe you and your friends are the only ponies who can understand and rewrite it. Princess Celestia''

''From one to another, another to one. A mark of one's destiny singled out alone, fulfilled.''

Twilight Sparkle: That doesn't make any sense. It doesn't even rhyme!

[End of Flashback]

Twilight Sparkle: I cast the spell so I could find out what it was, but nothing seemed to happen. But now I know something did happen. The spell has changed the Elements of Harmony! That must be why their cutie marks are all wrong!

Shadow: So just cast a counter-spell to switch them back.

Twilight Sparkle: Oh. There is no counter-spell!

Shadow: What?!

Tails: Why don't you just use that memory spell we made you use when Discord made you and your friends his queens of chaos?

Twilight Sparkle: I thought we agreed to not talk about that, presides, it's not their memories, it's their true selves that have been altered!

Knuckles: Zecora's cure for the cutie pox?

Twilight Sparkle: That won't work either...

Spike: Well [sighs], maybe it won't be so bad. Maybe our friends will grow to like their new lives.

Twilight Sparkle: No, Spike. [tears up] They're not who they are meant to be anymore. Their destinies are now changed, and it's all my fault. [runs off crying]

Cream: TWILIGHT, WAIT!!! [sighs]

Sonic: Well, I guess we need to help her with this. Sorry Egghead, need to make this a quick one. [Homing attacks into the Egg Mobile]

Dr. Eggman: [grunts] I completely understand!

[Dr. Eggman is knocked into the distance, screaming]

[Back at Golden Oaks Library, Twilight was laying on her bed, having gone into depression]

[Twilight Sparkle]

I have to find a way

To make this all okay

I can't believe this small mistake

Could've caused so much heartache

Oh why, oh why?

Losing promise

I don't know what to do

Seeking answers

I fear I won't get through to you

Oh why, oh why?

Twilight Sparkle: [echoing] A mark of one's destiny, singled out alone, fulfilled. [normal] [gasps] Wait a second, that's it! I understand now! I know how to fix the spell!

Sonic: You do, nice! Let's head back to the library!

[The Mane Six and Team Sonic head back to the library]

[grabbing the spellbook, Twilight begins to rewrite the spell]

Twilight Sparkle: From all of us together, together we're friends. With the marks of our destinies made one, there is magic without end! [breathes a sigh of relief]

Amy Rose: That should do it.

[just then, the Elements of Harmony sparked to life before shooting beams at Twilight, who looked around in shock and confusion, not even noticing when her element started shooting similar beams at her friends, eventually, all six ponies were surrounded by their own sphere of light]

Team Sonic: [covering their eyes]

[the library glowed brightly, with Spike, Applebloom, Sweetie Belle, Scootaloo, Nyx, Snowdrop, Trixie, Rouge, Silver, Blaze and the Chaotix noticing from outside, with them running towards it once the light vanished]

Sonic: Wow! That was some light show!

Cream: [gasps] What happened?

Spike: [bursts into the library] We saw light from outside, what- happened...?

[The Mane Six were nowhere in sight, they had completely vanished, leaving only six scorch marks on the wood floor in the shape and pattern of the girls' cutie marks]

Team Sonic: [exclamations of shock]

Tails: No... You don't think...

Knuckles: Girls!

[Amy falls to her knees while Cream tears up, Shadow looked mortified]

Tails: Oh Sonic, how could this happen? It's just not fair. Now we'll never see them again. They're were... they're were our friends. We'll miss them. They can't be gone. [bends down his knees and starts crying]

Sonic: [just sighs sadly]

[Twilight and her friends wake up to find themselves in in a strange, ethereal space full of stars and nebulae]

Twilight Sparkle: [echoing] Hello? Where are we? What is this place?

Pinkie Pie: [echoing] Huh? [gasp] Cool! Echo!

Rainbow Dash: [echoing] Holy cow, are we in Space?!

Applejack: [echoing] Uh, Twilight, was the spell suppose to bring us here?

Fluttershy: [echoing] I kinda wanna go home now...

Rarity: [echoing] Can we even go back?

[Celestia appears]

Princess Celestia: [echoing] Congratulations Twilight, I knew you and your friends could do it. [hugs Twilight]

Twilight Sparkle: [echoing] Princess? I don't understand, what did we do?

Princess Celestia: [echoing] You 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 you all do. The lessons you've all learned in Ponyville and with Sonic and his friends have taught you well. You have all proven that you're ready.

Mane Six: [echoing] [confused] Ready? Ready for what?

[Celestia leads the Mane Six down a pathway of stars as dozens of images float by, depicting key moments from their past adventures]

[Princess Celestia]

You’ve come such a long, long way.

And I 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 to see all the ways you’ve all made me proud of you.

It’s time now for a new change to come.

You’ve all grownup and your new lives have 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 destinies!

[At that moment, a light from each mare’s heart matching their elements emerged and began to swirl around them while a pulsing white light grows from their centers and heads. The Mane Six lifted into the air, the lights blanket and envelop them, and they disappeared in a brilliant flash, like the supernova of a star]

[Back in Ponyville, Team Sonic and the others saw six bright lights in the night sky. Each of them looked very similar to cutie marks they knew. The lights descended in front of the library and as the light faded they could make out the shapes of six very familiar ponies]

Tails: What's that?

Sonic: Girls? Is that you?

Knuckles: It better be.

[The Mane Six get up, now a little taller and now with both wings and horns]

Everyone sans the Mane Six: [gasps in amzemeant]

Sonic: Whoa, I was NOT expecting this.

Twilight Sparkle: [gasps] Sonic! [Sonic goes over and hugs her]

Applejack: [shocked] Wha... I-I've never seen anything like this.

Knuckles: Me neither.

Rainbow Dash: Ha! We've all got wings now! Awesome! Now we can all be flying buddies! [laughs]

Shadow: Huh, gotta say, I'm amused.

Rarity: Why, we've all become Alicorns. I didn't even know that was possible.

Amy Rose: I didn't either.

Pinkie Pie: [screaming while flying] Alicorn party! [uses her newly aqquired magic to make confetti and balloons appear while she blew on a noise maker]

[crowd cheering]

Tails: Incredible...

Cream: Wow... How did this happen?

Fluttershy: [looks at her new horn] I don't know... But we all look just like princesses.

Princess Celestia: [flying down] That is because you are princesses.

Everyone: Huh?!

Pinkie Pie: Hold on a second! [quickly uses her magic to make a glass of water appear before drinking it and spitting it out]

Twilight Sparkle: A... A princess? [looks at her friends] Each of us?

Princess Celestia: Since the day you all met here in Ponyville, you've all displayed the charity, compassion, devotion, integrity, optimism, and of course, in each of your own way, the leadership of a true princess.

Twilight Sparkle: [concerned] But... does this mean I won't be your student anymore?

Princess Celestia: Not in the same way as before. I'll still be here to help and guide you, and I'll just say that you don't have to abandon your dreams or responsibilities here, but we're all students to all of you now, too. You six are an inspiration to us all.

[Celestia, Spike, Sonic, his friends and the others bow before the Mane Six, Cream and the Cutie Mark Crusaders were crying tears of joy]

Twilight Sparkle: But... what do we do now? Is there a book about being a princess we should read?

Rainbow Dash: Does being a princess automatically make me leader of the Wonderbolts?

Fluttershy: What if my animal friends don't recognize me with this horn?

Rarity: Oh my, with the wings, I'll have to alter my entire wardrobe.

Applejack: Will my family have to move to Canterlot?

Pinkie Pie: Can I plan the next Grand Galloping Gala?

Princess Celestia: [giggles] There will be time for all of that later.

[the Mane Six looked at each other while smiling, their eyes slightly tearing up] [The next day, at Canterlot Castle]

Princess Celestia: We are gathered here today in celebration of a momentous occasion. My most faithful student, Twilight Sparkle, and her friends Applejack, Rainbow Dash, Fluttershy, Rarity, and Pinkie Pie have all done extraordinary things since Twilight came to live in Ponyville. They even reunited me with my sister, Princess Luna.

[Princess Luna smiles at her sister fondly]

Princess Celestia: But today, they did something extraordinary. Together, they created new magic, proving without a doubt that they are ready to be crowned Equestria's new princesses. Fillies and gentlecolts, may I present for the very first time, the Princesses of Harmony!

[The doors open revealing the Mane Six wearing wearing beautiful gowns, Rainbow Dash, Applejack, Fluttershy, Pinkie Pie, and Rarity all wore necklaces modeled after their elements, several ponies were walking behind them, carrying flags on their backs]

[Choir]

The Princesses of Harmony cometh

Behold, behold

These Princesses here before us

Behold, behold, behold

Behold, behold (behold, behold)

The Princesses of Harmony cometh

Behold, behold (behold, behold)

The Princesses are

The Princesses are here!

[Twilight was given a crown modeled after her element while the other got tiara’s similar to Luna’s or Cadance]

[crowd cheering]

Princess Celestia: Shouldn't one of the princesses say something?

Twilight Sparkle: Oh. Um... [clears throat] A little while ago, my teacher and mentor Princess Celestia sent me to live in Ponyville. She sent me to study friendship, which, aside from the fews friends I knew there since foalhood, was something I didn't really care much about at the time. But now, on a day like today, I can honestly say ''we' wouldn't be standing here if it weren't for the friendships we made with eachother and with our Mobian friends. We each taught eachother something about friendship, and for that, I will always be grateful. ' Today, we consider ourselves the luckiest ponies in Equestria. Thank you, friends. Thank you, everypony!'''

[crowd cheering]

[Back inside, the Mane Six took time to spend time with the friends and loved ones, Twilight was approached by Shining Armor, Princess Cadance, Sonic, Spike, and her parents]

Shining Armor: Twilight, I'm so proud of you.

Twilight Sparkle: [notices a tear on Shining's check] Are you crying?

Sonic: Sure seems like it.

Shining Armor: Of course not! It’s liquid pride! Totally different thing.

Sonic: [whispers] Like that's true, but hey, that's a good way to express himself.

[Twilight just smiles]

[Applejack was with her family, with Granny Smith, Applebloom, Big Mac, Babs Seed and Braeburn among others, including Knuckles]

Applejack: Now don’t you threat nothing Granny, I won’t be forgetting my roots.

Granny Smith: Oh, I know young’un. It'll take a lot more than a fancy horn and a pair of wings to make an Apple forget where she comes from.

Knuckles: I think what she's trying to say is, even though you look a little different on the outside, on the inside, you're still you.

Applejack: Right. [to Applebloom] Now, Applebloom; I’m going to have a lot of new responsibilities and since you’re getting older, I'm counting on you to help keep the farm running when I'm away. But I promise that I'll always come home when you need me and I'll be there for every reunion.

Applebloom: You can count on me sis!

Applejack: Oh, and Big Mac, you'll keep a eye on her?

Big Mac: Eeyup!

[Rarity was with her parents, Scootaloo and Amy]

Hondo Flanks: Who would have thought that all this time I called you princess that it was prophetic?

Cookie Crumbles: Now your dreams have come true.

Rarity: Well I still need to find Mr. Right but I just want to say that I couldn't have wished for a better family to call my own.

Amy Rose: You're proud of yourself too, right? I mean, this is practically what you've been dreaming of your entire life.

Rarity: Indeed so Amy. [to Sweetie Bell] Sweetie Bell, now that I have fulfilled my destiny, I cannot wait to see what yours holds. If you need my help with anything, just let me know.

Sweetie Belle: [crying tears of joy] I love you big sister!

[Rainbow Dash was with Scootaloo and Shadow]

Rainbow Dash: So Shadow, was there something you wanted to tell me?

Shadow: [sighs] I'll admit, even though you and I have had our differences, you're actually pretty cool.

Rainbow Dash: [gasps] Nice!

Scootaloo: So, you're still going teach me how to be a great flyer like you?

Rainbow Dash: I'd never leave you hanging kid.

Scootaloo: Rainbow Dash, you are the most awesome princess ever!

[Shadow just smiles as the scene switches to Pinkie, who was with her family, Tails and the Cakes]

Pinkie Pie: Hey everypony, I’m so glad you’re all here.

Cloudy Quartz: Pinkamena, we're all so proud of you.

Igneous Rock Pie: Who would have thought that from just a humble rock farm a princess would be born?

Limestone Pie: I still can’t believe my sister's a princess!

Marble Pie: Guess it goes to show that you never know who'll become what.

Tails: True that.

Pinkie Pie: [to the Cakes] Now, because I know Princess Cadance did some foalsitting in her time, I want you to know that you can still count on me as your go to foalsitter.

Mrs. Cup Cake: Oh, Pinkie.

Mr. Carrot Cake: You don’t know how happy that made us, the twins love you.

Pumpkin Cake/Pound Cake: Prwincess!

[Fluttershy was seen with Angel, Cream and Cheese]

Fluttershy: You know, after all these years, I never thought I'd be brought into royalty.

Cream: Well Miss Shy, life is full of surprises, also, if you want, maybe me and my mother can watch over your animal friends when you can't be there.

Fluttershy: [tears up] Oh Cream, thank you!

Cream: What can I say, always happy to help.

[The Mane Six came back together]

Applejack: Way to go with that speech Twilight.

Pinkie Pie: Best coronation day ever!

Fluttershy: I love you girls.

Twilight Sparkle: I know, we all share the same feelings.

[The Mane Six all hug as Sonic and Amy watch nearby]

Amy Rose: Oh Sonic, isn't this lovely?

Sonic: [sighs] Yeah Amy, it really is, so glad we stuck with them till the end.

Amy Rose: Just goes to show that life is full of surprises!

Sonic: [laughs] Couldn't agree more.

[Outside Canterlot, Eggman was watching the coronation with Orbot and Cubot]

Dr. Eggman: Oh, this just got a lot more intreresting. [laughs quietly to not attract attention]

Cubot: What a swell adventure! Sure hope there's more next season!

Orbot: Just think of the hundreds more stories to be told using the same characters and multiple locations; the possibilities are limitless!

Cubot: Just to be on the safe side, maybe we should start an internet petition.

[Back in Canterlot, each new princess rode in her own carriage]

[Twilight Sparkle]

Life in Equestria shimmers

Life in Equestria shines

And I know for absolute certain

[Main cast and crowd]

That everything (that everything)

Yes, everything (yes, everything)

Yes, everything is certainly fine

It’s fine

[The Mane Six all took off for their first flight together]

Mane Six: Yes! Everything’s going to be just fine!

Trivia

 * The last few scenes has cameos from several Sonic and MLP characters.
 * The beginning of the episode is taken from Sonic Lost World.