The Princesses of Harmony

Summary
When Princesses Celestia and Luna mysteriously disappear right before the Summer Sun Celebration and mysterious vines invade Ponyville and take control of Eggman's robots, the newly crowned Mane Six and Team Sonic, along with Sunset Shimmer and Discord must figure out what's going on, during all of this, the Mane Six discover the origins of the Elements of Harmony, and a old friend of Tails finally returns.

Differences

 * Applejack, Rarity, Pinkie Pie, Rainbow Dash and Fluttershy stay behind with Twilight in Canterlot due to them being princesses as well in this timeline.
 * The Mane Six all use the alicorn potion to go into the past while Team Sonic tries their best to defend Ponyville from the plundervine and Eggman's robots.

Transcript
[The scene cuts to Canterlot Castle, Team Sonic were looking at something when the Mane Six walk in, all six of them were wearing regalia modeled after their elements]

Twilight Sparkle: What are you looking at?

Sonic: Oh, hey your highnesses. [chuckles to himself]

Rainbow Dash: You do know you could just call us by our actual names, right?

Applejack: Yeah, I mean, we all know each other after all.

Sonic: Sorry, force of habit.

Amy Rose: Whoa, you're actually have full on regalia now?!

Fluttershy: Yeah, we weren't gonna, but Rarity insisted.

Rarity: Well, we have got to embrace our royal titles eventually.

Cream: I mean, you six do look pretty nice in it.

Pinkie Pie: I know right!

Twilight Sparkle: Oh, what exactly are you looking at?

Knuckles: Oh, just this.

[Turns out Team Sonic was looking at new the new stain glass window commemorating the Mane Six's ascension and coronation, along with Star Swirl the Bearded's spell book and a book with their cutie marks on the cover underneath]

Fluttershy: Wow...

Rarity: We look amazing. They've really captured our regality.

Twilight Sparkle: I suppose.

Rarity: Oh, don't be so modest. It's everypony's dream to someday wear a crown and have their coronation ceremony preserved in stained glass for all to see. [sighs]

Rainbow Dash: I don't know if it's everypony's dream.

Pinkie Pie: Most of my dreams are about frosting! [slurp] Ohohohoho...

Cream: [looks at the time] Oh goodness, we'd better get going. We don't want to miss our train.

Blaze: Cream's right. I don't know about you, but there's still a lot of work in Ponyville to be done.

Silver: Yeah, the official celebration may be here in Canterlot, but Mayor Mare put us in charge of the local celebration back in Ponyville in your absence.

[The Mane Six look a bit downcast by this]

Rouge: Don't look like that, girls. You get to be right there with the other Princesses when Celestia raises the sun.

Twilight Sparkle: And we're honored.

Pinkie Pie: Really, we are.

Rainbow Dash: It's just that the Summer Sun Celebration is what first brought us all together. Well that and some dimension hopping.

Rarity: I think what she's trying to say is, it just doesn't feel right not getting to spend such a special day with our mobian friends.

Amy Rose: It doesn't feel right to us either, Rarity. If the Mayor wasn't so desperate for our assistance, we'd most certainly stay here in Canterlot. And of course we do understand that your royal duties must come first.

Tails: The Summer Sun Celebration may have brought us together, but you six have something much bigger that'll always keep uyou connected. Exhibit A: The six of you are united by the Elements of Harmony.

Sonic: Tails is right, but don't worry, no matter what happens, we'll be friends forever, no amount of royal duties is ever gonna change that. Right, guys?

Team Sonic: [general agreement]

Sonic: Right, Shadow?

Shadow: Hmm, I suppose. [grins]

Cream: You should take that as a yes.

[Team Sonic and the Mane Six reached the entrance of the forest]

Rarity: Seems like only yesterday we were heading into these woods to find the Elements of Harmony.

Sonic: Seems like only yesterday I joined you six so I could find my friends. [looks at Knuckles, Cream, Tails, Amy and Shadow, with Rouge, Silver and Blaze nodding]

Twilight Sparkle: Yeah, I don't know what we're going to face in there. But whatever it is, I know we need to face it together.

All: [agreeing]

Knuckles: Alright then, let's go!

[The heroes walk into the forest, eventually coming across a creek]

Cream: How do we get across?

Twilight Sparkle: We can use those to cross.

Pinkie Pie: Good idea.

[The Mane Six jump onto what appears to be some rocks, only to accidently wake up a sleeping cragadile]

Mane Six: [yelps]

Amy Rose: [gasps] A cragadile! Run for your lives!

Cragadile: [roars]

[the cragadile advances on the Mane Six, but Silver uses his psychokinesis to restrain it long enough for Sonic, Tails, Knuckles, Shadow, Amy and Cream to get the Mane Six out of their situation]

Twilight Sparkle: That was close.

Applejack: [sighs] A little too close, if you ask me.

Fluttershy: Yeah...

Rouge: Are you girls alright?

Twilight Sparkle: We're fine, I guess.

Rarity: How did we not notice that thing.

Silver: I don't know, but please be more careful.

Sonic: Yeah, who knows what else is gonna to come after us? [thinks about something] Actually, you know what, maybe it wouldn't be such a bad idea for the Mane Six to go back to Ponyville and let us look for the Tree of Harmony without them.

Mane Six: [shocked] What?!

Applejack: Why?

Sonic: Well, for starters, you nearly got eaten by a cragadile.

Rainbow Dash: We all did. He wasn't just after us.

Sonic: Sure, but... well, my friends and I aren't princesses, well, technically Blaze is, but that doesn't really matter.

Blaze: Hey!

Pinkie Pie: What's that got to do with anything?

Sonic: Princess Celestia and Princess Luna are gone. If something happened to you six, I-I just don't think Equestria can risk losing another princess.

Knuckles: Granted, there is Princess Cadance, but she's the leader of the Crystal Empire, which is technically it's own nation.

Tails: Yeah, Sonic and Knuckles make a valid point. Even if we do manage to save the Tree of Harmony, it won't necessarily mean Princess Celestia and Princess Luna will return.

Shadow: Yeah, Equestria will need someponies to lead in their absence.

Twilight Sparkle: But the Tree of Harmony! We're the only ones who have seen it and know what it looks like.

Amy Rose: Huge tree, cutie marks on the trunk, probably being attacked by something hideously awful? Yeah, I'm pretty sure we'll know it when we see it.

[The rest of Team Sonic nod in agreement]

[The Mane Six look down as tears trinkle down their cheeks]

Rarity: All of you feel this way?

Fluttershy: Feel like we shouldn't be here?

[Sonic, Tails, Knuckles, Amy, Shadow, Rouge, Silver and Blaze nod]

Cream: It's probably for the best... [whispers] I'm so sorry...

[The Mane Six leave as Spike follows]

Cream: I feel bad... [Cheese pats her on the back]

Amy Rose: Don't worry Cream, at least we'll know they're safe.

Cream: I suppose so.

Sonic: Yeah, now come on, the Tree of Harmony isn't gonna save itself.

[Team Sonic run deeper into the forest]

Discord: [humming]

Cherry Berry and Comet Tail: Help! Help!

Twilight Sparkle: Discord!

Discord: You're welcome! Hmph.

Dr. Eggman: [surprised] Back already?

Sunset Shimmer: No luck finding the tree?

Rainbow Dash: Well, we ran into some trouble.

Fluttershy: And Team Sonic decided it would be best if we returned to Ponyville while they continue the search.

Twilight Sparkle: Yeah, Equestria will need us if Princess Celestia and Princess Luna don't return.

Discord: I'm just surprised that you agreed to their plan. I never thought you'd be the kind of ponies who would think they were better than everypony else.

Twilight Sparkle: We don't think we're better than anypony!

Pinkie Pie: Yeah!

Discord: Oh, well, how silly of me to assume that you six would think that. All you six did was choose to keep your precious princess selves out of harm's way while your mobian riends thrust themselves right into it. I'm sure you'll all be the best of pals again when they return from their terrifying yet deeply bonding experience that they're having without you. [chuckles]

[At that point, the Mane Six rushed back into the forest in annoyance]

Trixie Lulamoon: Nice going Discord.

Rarity: We never should have agreed to come back here.

Spike: Come on, girls. Discord may be reformed, but he's not that reformed. He's just trying to get under your skin.

Twilight Sparkle: Well, it's working!

[Team Sonic was walking through the forest]

Silver: Anyone else starting to think this is a lost cause?

Knuckles: Yeah, we're almost at Celestia and Luna's old castle. Maybe whatever the Mane Six saw when they took that crazy potion wasn't real. Maybe there is no Tree of Harmony. Maybe–

Sonic: Maybe it's right down there.

Knuckles: [gasp] It can't be!

[Team Sonic stare]

Cream: How are we supposed to get to it?

[Tails finds some stares]

Tails: Maybe these stares will help.

Sonic: Nice observation Tails.

[The Mane Six and Spike walk together]

Spike: Are we there yet?

Rainbow Dash: For the hundredth time: No.

Twilight Sparkle: I don't know where we are. We're lost.

Fluttershy: We never should have left our friends.

Spike: We can't just give up. Maybe if I get up there, I'll be able to spot 'em.

[Spike climbs a tree]

Spike: Well, what do you know?

[Suddenly, Spike hears a hissing sound]

Spike: Girls? Twilight?

[Spike sees the Plunder Vines spewing spores at the Mane Six]

Mane Six: [coughing]

Spike: [gasp]

[Meanwhile]

Cream: [gasp] I think it's dying!

Knuckles: So let's save it already!

​[Knuckles tries to land a punch but gets thrown back]

Sonic: Nice try Knux, but I've got this.

​[Sonic tries to spindash into it but gets knocked back as wel]

Sonic: Heh- Whoa! Oof!

Blaze: Valiant efforts on both your parts, but the tree remains in jeopardy.

Shadow: And I suppose you've got a better idea?

​[Blaze tries to think but has nothing]

Shadow: That's what I thought.

Amy Rose: What do we do? Is there any way to save it?

Cream: Well, I know six ponies who would know what to do. [tears up] But we sent them home...

[Tails, Knuckles, Shadow, Rouge, Silver, Blaze and Amy look at Sonic crossly]

Sonic: What?

Knuckles: [angrily] It was your idea, Sonic!

Sonic: [angrily] We all agreed it was the best thing, Knucklehead! We were trying to protect them.

[They hear Spike]

Spike: Oof! Ow! Ugh! Ow! Whoa! Ugh! [whinny]

[He lands near the ponies]

Spike: Girls! Trouble! Help!

​[Team Sonic gasps]

[Meanwhile, the Plunder Vines surround the unconscious Mane Six and hiss]

[One of the vines is about to bite down on them when Team Sonic showed up, they were about to fight the vines when a bright light shined near them]

Sonic: What the...

[a figure emerged]

???: You will not hurt them!

[The vines plunge at her but she uses her powers to take control of them and send them away, the light fades and it turns out to be Cosmo, who was last thought to have died sacraficing herself to save the galaxy]

Cosmo: [to the unconsious Mane Six] It's okay, you're safe now.

Tails: [gasps before tearing up] A-Am I dreaming? It's not possible... COSMO! [runs up to her]

Cosmo: [gasps] TAILS! [hugs him]

Tails: [sobbing] I missed you so much!

Cosmo: I know, it's been such a long time...

Amy Rose: [sniffles] Well ain't that the sweetest reunion you ever saw?

Spike: Uh, I'm confused, who is that, and why does Tails know her?

Sonic: It's a long story...

[the Mane Six regains consciousness and stand up]

Twilight Sparkle: What happened?

Cream: Girls, you're okay!

Amy Rose: I sure am glad you came looking for us.

Rarity: Not as glad as we are that you found us.

Sonic: Yeah... [looks guilty] I'm sorry I suggested you'd go back to Ponyville, we're just simply lost without you six.

Silver: Yeah. Equestria may need its princesses...

Cream: ... But we need our friends.

Cosmo: Yeah, and it's good to see you all.

Sonic: Yeah Cosmo, it's been a while, huh?

Fluttershy: Cosmo? Who is that?

Tails: We'll explain later, for now, just know that she's on our side.

Pinkie Pie: Okay! So, are we gonna save the Tree now, or what?

Sonic: Alright then, let's go team!

Team Sonic/Mane Six/Cosmo: Right!

[Team Sonic, Cosmo and the Mane Six come out of the Everfree Forest when Discord shows up]

Discord: Bravo, ladies and gentlemen, bravo! How ever did you save the day this time? Blast the beastie with your magic necklaces, I presume? Where are those little trinkets of yours? You know, the ones you use to send me back to my extremely uncomfortable stone prison?

Applejack: [sigh] Gone.

Knuckles: Yeah.

Discord: Gone? Gone?

Twilight Sparkle: We had to give them up.

Cream: For the sake of Ponyville and ourselves.

Discord: Well, that seems kind of weird.

Fluttershy: But our friendship remains. And if you want to remain friends, you'll stop thinking whatever it is you're thinking and help us clean up.

Discord: Fine. [holds up a picture with a window on it] But I don't do windows.

Applejack: One thing I don't get. Why did all this happen now?

Silver: I was kinda thinking the same thing.

Discord: I have no idea. Those seeds I planted should have sprouted up ages ago.

[Everyone stops walking]

Twilight Sparkle: What did you say?!

Discord: [dumbfonded] Oh, why should I try to explain it when you can see for yourselves? [hands the Mane Six the potion with his tail]

[The Mane Six drink the potion and their eyes turn white. Flashback to when the Princesses first imprisoned Discord]

Princess Celestia: Playtime is over for you, Discord!

Discord: Oh, I doubt that. [munching] Hungry? [voice over] Well, obviously things didn't go according to my original plan. My plunderseeds should have stolen the magic from the Tree of Harmony and captured Princess Celestia and Princess Luna thousands of moons ago. Alas, it seems the tree had enough magic to keep the seeds from growing up big and strong. Until now, that is.

Twilight Sparkle: You realize this is information we could have used hours ago?!

Rainbow Dash: Yeah, that could've saved us a lot of time!

Discord: What? And rob you of a valuable lesson about being princesses? What kind of friend do you think I am?

[Discord snaps his fingers, snapping the Mane Six out of the flashback]

Sonic: So you were holding out on us!

Amy Rose: Yeah, what the heck Discord?!

[Shadow's eyes were red with fury and Knuckles had his fists up]

Discord: Now, I know that sounds bad but- [stops talking when he sees Amy get her hammer out] YIKES! HEDGEHOG GIRL, WAIT! PUT DOWN THAT HAMMER! [runs away]

Knuckles: GET BACK HERE! [chases after him with Amy and Shadow]

Dr. Eggman: Well, since my robots are back under my control, I might as well get out of here. [summons his egg mobile] See you at our next battle Sonic. [flies away]

Sonic: Oh trust me Eggface, we'll be waiting.

[Later, in Canterlot, a huge crowd was gathered]

[The Mane Six, now with new crowns and regalia, stand ready]

Princess Celestia: Citizens of Equestria. This Summer Sun Celebration not only celebrates the defeat of Nightmare Moon but the return of my sister, Princess Luna.

[She raises the sun and Luna lowers the moon as the Mane Six use their combined magic to perform a Sonic Rainboom on the stage as they fly off]

Sonic: I knew they would get a hang of their alicorn magic sooner or later!

Silver: Whoo-hoo!

Knuckles: Yeah!

Rouge: Alright!

Shadow: Hmm. [smirks]

Cream: Way to go, girls!

Amy Rose: That's my little ponies!

Blaze: Cool!

Tails: Good job, Princesses!

Recap
"Last time on Sonic Adventures in Equestria, still getting used to their new roles as alicorn princesses, the newly crowned Mane Six are surprised when Princess Celestia and Princess Luna mysteriously disappear right before the Summer Sun Celebration. As they try to figure out what happened to them, they receive word that the Everfree Forest has invaded Ponyville, if that wasn't bad enough, Team Sonic found out the these mysterious plundervines have taken control of Eggman's army, the Mane Six accuse Discord of causing the mess, but since Discord is now reformed, it couldn't have been him, if even some of the heroes still don't trust him, with help from Zecora, the Mane Six use a potion than only alicorn magic can activate, which sends them over 1,000 years to the past, where they first hand how Luna first turned into Nightmare Moon, either way, will our heroes figure out a way to stop the Plundervines from destroying Ponyville and will Celestia and Luna be found in time, find out next on Sonic Adventures in Equestria."

Trivia

 * Cosmo, who last appeared in Sonic X, makes a unexpected return to help with the plundervines.
 * Metal Sonic is shown to be immune to the plundervine's effects on Eggman's machines.