RainbowDoubleDash's Lunaverse/WMG

WARNING: Because this is a shared universe that could be added to by anypony, whatever is posted here is essentially a Schrodingers Gun to use be it inside or outside of the cultivated Lunaverse. That being said, anything in here is to be treated as an unmarked spoiler unless explicitly Jossed, and even then is fair game for anyone to write about, so you have been warned.

Altwilight will create a cult bent on restoring the Celestian Timeline.
After the planned Crisis Crossover, Twilight will either be completely aware or with suppressed memories of the timeline that was. Without the Mane 6 or Celestia to keep her in check, she makes it her goal to revolutionize the Lunaverse into what she saw in the Celestial Equestria, and uses her formidable command over magic and minds to rapidly gain support.

There will be a fight between Corona and Nightmare Moon at some point
Because it's cool, and because we all want to know the answer.

Luna!Twi ends up being Corona's Dragon along with Zecora.
Who better to show Twily real magic than THE most powerful pony around? It would be a nice dark mirror to canon too.
 * This assumes that Twilight is completely insane. Like the rest of the Lunaverse versions of the Mane Six, her less palatable traits have been dialed up just a notch and her harmonic traits dialed an equivalent amount back. She's a sheltered, naive and mildly delusional workaholic on the run from being told to take a vacation by sympathetic parents, not Starscream.

Applejack will do a Heel Face Turn and become a Defector From Decadence.
She doesn't seem to have completely gone over to gleeful, bullying evil like Apple Bloom. An Armor Piercing Question in the right place and time could be the trigger that opens her eyes to the truth.
 * Seriously, what is with the belief that Applebloom is Diamond Tiara 2.0? She hasn't at any point acted significantly out-of-character compared to her usual self. In Longest Night, she's antagonistic towards Trixie, who had been arguing with her sister. She was a sore winner, is all. Meanwhile, in Boast Busted, she's restricted to giving the evil eye to Carrot Top every now and then, which is certainly not out of line with how she acted in the episode Call of the Cutie. My point is that people seem to have blown a few lines wildly out of proportion.

Alt-Twilight will form her own group of Elements.
Rather than commit suicide by going anywhere Corona, Twilight will prove her worth to Luna and her brother by assembling what she believes to be more fitting bearers than the Lunaverse Six. Given that she's kind of naive and a touch touched, her 'perfect' army will in fact be slightly dysfunctional at best owing to her over-reliance on dictionary meanings.

Luna cut a deal with Discord.
Luna may or may not have been jealous for her sister's attention, but also worried about her being the single thing keeping Equestria out of harms way. So when Discord came to town and enforced his rule of chaos, Luna offered him amnesty and regard in Equestrian court to end his reign of terror on amicable terms and keep her sister out of the line of fire. Discord accepted, then drove Celestia to madness, forcing Luna to seal away her sister to keep her safe from herself, and gained the free passage and private audience with the Princess whenever he feels like it.

The Lunaverse can be traced back to the original G1 series, G4 being a Pandorican reboot.
Due to the mention of Tirek and other call backs from deep within the franchise, the Lunaverse is what became of the world of Megan, the rainbow bridge, and the ponies of yore. The mainline verse is an optimized fork where events and the choosing of the modern Elements of Harmony were gamed to be the golden timeline, where as the Lunaverse evolved more naturally.