Optional backstory: A cute lone horse jumped from planet to planet growing magic and creating more horses in her image, each are a facet of her own personality and abilities. She is God.
 
We get a 10 minute exposition of the alicorn galaxy. We find out that the planet where our ponies live was created by said alicorn race through fantasy magic. The alicorn race lived in peace for billions of years until one night something triggered a sun to explode and created a massive black hole that engulfed their whole galaxy. Few escaped. Luna and Celestia ran off to the planet of Equestria.
 
The blackhole is finally closing in on their little space and this time moving around the sun, planet and moon through space won't do it any good. Discord(a black alicorn) tells them of an ancient power they can harvest to finally close in the black hole.
 
Luna, Twilight & her friends go on a crystal-texture star cruiser around through space searching for this treasure.
They visit a planet full of nightmarish eldritch abominations and inside the spirit world/the underworld they find what they're looking for.
 
Luna gives them the power to polymorph themselves and use as much magic as they need. Twilight uses the elements of harmony to share all 6 of their personalities between them for quick thinking and wisdom.
They defeat every challenge they pass through ingenuity and desperation. What they fight are genuine horror-looking monsters with an undead alien spectral thematic.
They die twice and even their planet dies because they ran out of time. Luna and Twilight use their power to go back in time and Twilight gives her element of magic to Dash and makes sure she uses it responsibly.
They succeed, but they die. Eventually in the movie it is shown they revive after a thousand years pass.
 
There are no songs in this movie.
 
 
Let's flesh the world design some more. The alicorns don't live like they're on krypton with science and white cloaks. They live on colourful worlds with flowing magic rivers, edible flowers, golden, platinum, ruby, emerald castles and in a rich flora of roses, pansies, sakura blossom trees, etc. It's a goddamn utopia. The more childish, horse-like and creative, the better, like candy instead of flowers and sugar cubes growing on trees.
 
Their practice of magic and their style of fighting is anything but traditional attacks in the form of elementals and energy rays, waves, blasts. They summon telekinetic lightning through their body and through their magic they can subdue, enchant, hex/curse, even corrupt their opponents.
The magic types are arcane, light/dark and a huge plethora of meta spells like curses, enchants, transformation, time, warping.
 
Turns out the sun, moon and earth were slowly moving through space across the universe trying to get away from the black hole.
They get a map, a compass and a magical orb that detects chaos magic and they get guided to the realm with the kind of power needed to seal the advancing black hole.
They have some fun in space visiting exotic beautiful places, but their end-game is the chaos realm where everything is off-looking and dangerous.
 
With the elements of harmony Luna assists them in order to power up her friends allowing them to change into celestial beasts and practice magic at the level of Twilight.
Twilight with the eoh provides something more interesting never seen before. The mane6 share their virtues among one another, like Dash her courage, Twilight her intelligence, their quick wits and subconscious abilities etc. this makes them think in sync at a high level. Of course rarely it can go haywire.
 
Dropped plotline: They go inside the black hole to stop it. The black hole is magical itself and can corrupt everyone to serve its purpose. Including Celestia. The black miasma created Discord.
 
>They have some fun in space visiting/needing to through exotic beautiful places before reaching their end-game.
Literal dreamlike milky way. Where they go through a portion of space filled with milk
http://www.dailymotion.com/video/x2kw72x
 
The more locations I add, the extra time you have to put in. Each location needs around 7-10 minutes and absolutely no secondary characters.
40-60 minutes of the movie should be happening inside the primary world that they're after unless said otherwise.
 
They don't have to go off the edge of the universe, but things do get weirder the more they advance. They find a hole in which to sneak into the chaos realm.
As they near their destination they can see the fabric of space/time with their eyes. They go inside bubbles, rearranging their molecules, miniaturizing and changing into neuronal lightning impulses rapidly firing away on the cosmic web, they travel rapidly to the world between worlds.
 
The dimension is weird and screwed. Physics, chemistry, biology have their very own rules all resulting in an odd world. There's levels, the painted-like world, the ghostrealm, the blackness.
They die here once and Luna uses a gem to revive them.
After countless battles, puzzles, interesting locations and monsters like pic related. They find the source of power and use the EoH to extract and contain it.
 
The elements of harmony with the source of chaos interact in a bipolar manner, as one tries to control it and the other tries to run free. Eventually it manifests itself as sentient energy with equal parts of order and freedom, the kind of energy they need to stop the massive expanding black hole from voiding the galaxy.
 
Of course the moment that chaos magic touches the EoH their personalities screw up as they're no longer balanced correctly. Twilight acts like Pinkie and vice versa till we go as far combining their physical energies into 1 character. It takes a while to fix.
 
They die a second time trying to backtrack but they're lost in the darkness and the thick fabric of space they're stuck in. Out of alicorn gems things seem lost. They use the chaos-harmony magic to bring themselves back to life. Instead they keep trying to master their abilities by staying in the world and training. They create a new rift in space to come out of.
 
They manage to make it out 1) only to see nothing, their planet had been absorbed by the black hole leaving an empty space to ponder about. 2) it left debris of their planet and they see Celestia's magic essence floating about. 1+3) They get a serious spook out of realizing they are in the black hole but remain unaffected by it due to their chaos-harmony magic, they study it and learn how to stop it.
They've been stuck there for trillions of years as time passed differently for them and their bodies, making them immortal in that void realm. What seemed like seconds were millions of years.
 
Luna needs Twilight's help in turning back time trillions of years back and Twilight gives her element of magic to everyone (especially Dash) to use her leadership skills, planning, intelligence so they know what to do.
 
Luna and Twilight teleport the mane5 imbued with the chaos-magic at the right time and the right location in space right before the black hole absorbed them. (The past mane6 and Luna still stuck in the void.)
Luna & Twi cannot use the time travel spell again, ever. They stare at each looking a bit around realizing that the universe is dead, there's nothing to grow out of it. They have an intelligent dialogue for finding a solution to their problem. They do the unthinkable.
They contemplate existentalism and commit suicide, embracing the release of their consciousness into nothing and enjoying non-existence.
 
The mane5 go inside the black hole and we see what our imagination of a black hole is like(does the matter concentrate like a thin pasta or is it something more creative?). They send out an array of faster-than-light needles/grappling pseudopodes to grab the edges of the black hole to pull it together onto itself and then implode the black hole, killing them in the process.
They're all all dead.
 
Celestia celebrates them and they remain in history till they turn into something older than legends.
Celestia looks over a bunch of newborn fillies while giving her monologue, she finds a way to revive them and she says a few thousand years will take for them to form again, the disembodied voices of the mane6 giggle asking what are a few thousand years compared to an eternity?
The end?
 
1)
Slow end credits.
We see Mane6's parents breeding(through magic) generation after generation, each pony looking a bit more like the ManeSix.
Luna's revival is more special as she does it on her own.
 
2)Their magic essence are found and they get used to revive the mane6.
4) They come back through some contradicting loophole like using the time travel spell or something impossible like  Celestia realizes where they are, slows down time and goes to pick them up from the darkness in the chaos realm. Honestly some of these challenges could be specials or even movies of their own.
 
(Bonus scene we see Luna and the mane6 reviving)
The end.
(Bonus we get one final scene or a 20 minute deleted episode where everything is normal and they have adventures again, for Celestia made sure the ponies couldn't steer away from their intended goal as a simple fantasy utopia. The mane6 and the princess never feel alienated from their kingdom. Or like in Futrama time repeats itself and they're back to status quo when they were first born, but a new cycle)
 
(Deleted scene) Celestia employed a new breeding and cloning program where the ponies breed like rabbits, but she promotes natural selection by silencing 30/32 of the fillies till she reaches to that exact streak of dna till it's close enough and she clones it and re-breeds it. She attempts to directly manipulate the dna to create the mane6 and also her own race of alicorns, but it's no use.