Trying to put together an idea in my head here, crossing MLP with BTTF
Prelude
The CMC sneak into the stage where "Sapphire Shores and Zigfilly Follies" tour has set up their equipment, to try for a CUTIE MARK CRUSADERS ROCK BAND cutie mark.
Giant subwoofer, blasted off the stage.
Ring, time for school!
Cheerilee is taking them to see the old city hall clock, that was damaged by the first ever Sonic Rainboom, and everyone gets a flyer about it or takes notes or something.

Get Scootaloo on her own somehow (Apple Blossom and Sweetie Belle need to have something else they each have to do, not together)

Back in time Sequence
Probably set in Sweet Apple Acres near the clubhouse, though that makes it hard to do the twin pines / lone pine mall gag
Or maybe set in a mall where the Pie family's stone farm used to be - that would allow for the frightened family showing up in the barn!
Scootaloo runs into Spike
Spike explains the amulet
- a secret project that Twilight's been working on for Celestia, involving Equestria's history
Spike: I traded my favorite muffin recipe I got from Applejack, with the diamond dogs for the gems to make the amulet!
Scootaloo "Wait...muffin recipe......baked bads? D:
Diamond Dogs show up in a minecart
"THOSE MUFFINS WERE TERRIBLE!"
Diamond Dogs "shoot" Spike with slingshots and rock-stale muffins
Spike is KO'd
Scootaloo decides to rescue the amulet
Diamond Dogs demand the amulet, or they're gonna take it
Scootaloo - "Fine take it...if you can catch me!"
Chase 1
DD's arm a catapult with a giant baked bad cake
"Let's see if you dogs can do 88!"
Chase 2
SONIC TIMEBOOM (that exact effect, the zapping wavefront cone, then a rainboom shell, then it implodes back on itself and leaves a trail of blue fire along the path Scootaloo would have taken)
Diamond dogs are scattered all over the place.
Spike, or maybe one of the diamond dogs- "She disintegrated into fire?"
Doctor Whoof (suddenly arriving from off-right): "Wait, that's not fire *zzap* Ow, yes, not fire, that's um *puts hoof to mouth* artron energy, DEFINITELY artron energy." - "What?" - "Nothing! Nevermind, ah running!" *pzoom*

Scootaloo arrives in a much younger Sweet Apple Acres Pinkamena's stone farm
Crashes into the barn, startles family, which flees.

plot point: the photo, probably the one from the opening of the mane six- maybe Scootaloo is found and taken care of by a young Fluttershy, and so she misses the argument where Rainbow Dash defends her? It would be in character I suppose-

plot point: Someone needs to explain the timestream problems to Scootaloo, I'd prefer it to be Doctor Whoof, tho Celestia might also be a likely candidate....maybe she runs to Canterlot to ask Celestia about the amulet, can't get audience though, but the Doctor just happens to be there, and fills her in on the details?

Maybe Doctor Whoof can be wearing the analysis helmet Twilight uses on Pinkie Pie in Feeling Pinkie Keen, like Doc Brown is wearing in BTTF when Marty shows up?

plot point: like in BTTF, the amulet (flux capacitor) needs a power source only available in the present, not the past. Maybe it draws its power from the Elements of Harmony, which would still be in their thousand year sleep at this point? Think we can rely on Dash's first sonic rainboom as an alternate powersource, since ponies can control the weather and deliver lightning bolts on demand, and it's a one-off, so the timing has to be exact.

plot point: Convince Rainbow Dash to compete in the pegasus races against Biff. (Clyde? more horse related that way...do the colts in the pegasus race have names?)

At the school dance, Scootaloo performing Johnny B Goode with a filly Sapphire Shores.
And 80s Cheerilee is a student dancing there.
And maybe in the background, in the surrounding woods, Princess Celestia and Dr Whoof watching the events unfolding or something. XD

Returning to the future:
Ponyville Clocktower
Time jump powered by Dash's rainboom! THAT hits the clocktower as the power source that sends her back. (because a bolt of lightning is far too easy to get, just have a weather crew pegasus buck a stormcloud)

Back at the clocktower present
Derpy flies overhead.
fl-fl-FLASH, Scootaloo arrives back, startling Granny Smith (she has ALL the luck with Scootaloo, doesn't she?), skidding into the library, knocking the books down
Twilight: "Scootaloo? ...are you okay?" - "Yeah, sorry-" - "Wait, is that the amulet I've been working on?" - "Yes! I mean no! I mean- it was....it will be- not right now! I gotta go, I gotta see if Spike is okay! *flee*" - "But-" *Scootaloo is gone* *Twilight smiles, picks up a quill and a scroll, and starts writing*

Back at the orchard (mall? market? Whatever)
Scootaloo arrives, looks down, sees Spike go down under a hail of petrified pastry
Sees herself go "NO!" jump out, and grab the amulet
Sees herself punch through the timeline
Runs down, to talk to Spike.
Princess Celestia shows up!
Explains that what happened was why she commissioned the amulet (self-fulfilling paradox)

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Okay, there, that's all written. Now I gotta find a way to storyboard it.
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22 MINUTE EPISODE FORMAT:
Teaser: 1min30s (wildly variable)
Intro: 35s EXACTLY
[commercial break]
First Act: 7 minutes minus teaser, or around 5.5 minutes (episode header credits run 30s)
[commercial break]
Second Act: 7 minutes
[commercial break]
Third Act: 7 minutes
End Credits: 30 seconds