Title: I'm You, You're Me, and We're All Together
Main characters: The Mane Six, several OC's from CRISIS: Equestria (They all belong to GanonFLCL.)
Genre: Alternate Universe, Dark, Adventure, Romance, Slice of Life.
Canonical Placement: During Chapter 24 of CRISIS: Equestria, specifically near the end of Red Velvet's song.
Changes from the Story Cannon.
Silvertongue has already absorbed the power of Nihila by this point, however he never revealed that the Mean Six were clones, and instead ordered them to kill the main six now that he had no use for them.

Premise:
Rainbow Dash arrives just as Velvet finishing singing and attempt's to rescue her friends. Sadly she accomplishes absolutely nothing against Velvet and get's sucked into her fear aura. However, Rainbow's presence inspires Pinkie Pie to new heights of happiness, allowing to her temporarily break out of Velvet's fear aura. Velvet attempt's to fight back by forcing her influence onto Pinkie's friends in order to strengthen herself through their fears. However, she starts to get drunk on her power and ends up sucking in her own sisters as well.

Pinkie purposely get sucked back in and spreads her positive influence to the rest of her friends. Rarity, being the first to break free, uses her magic to strengthen everyone else (excluding their enemies), Twilight awakens next and manages to use her own magic to take control of the aura away from Velvet, pulling off a more controlled version of her magic burst similar to the one she had as a foal. Velvet desperately tries to regain control by feeding off her sister's fear, but as the rest of the Mane Six and their friends awaken, they each start to fight back against Velvet with their respective powers.

Starlight however, regain consciousness and-after berating Velvet for attacking her and promising to torture her later-wakes up Insipid, ordering her use Rarity's power to heal her sisters as well. They all attempt to take back control of the fight, but Twilight motivates her friends with several memories of their past fight's against Nightmare Moon and Discord. After taking full control of the aura, Twilight uses their combined power to manifest mental versions of the Elements of Harmony, attacking the Mean Six all at once. However due to them being clones of the six, firing the Elements at them brings unexpected results, as each one of the Mean Six is adsorbed into the Main Six's minds!

Insipid is pulled into Rarity's

Grayscale Force is pulled into Rainbow Dash's

Starlight Shadow is pulled into Twilight Sparkle's

Havocwing is pulled into Fluttershy's

Curaçao is pulled into Applejack's

Red Velvet is pulled into Pinkie Pie's

The Mean Six are then locked away in the subconscious levels of the Mane Six's minds, each in a cage specifying their Elements, while in the outside world the Mane Six are revealed to have their counterparts powers along with their memories! Discovering what their master Silvertongue has plans for them, they make their biggest priority to not only get to Hope's Point and alert the Queen, but find a way back to their world before it's too late!

But Twilight's magic can't keep the mean Six caged forever, what devious methods will the groups counterparts resort to for their freedom?

3316383 Who says they have to escapte from the Mane 6's minds? Maybe they like it in there to begin with?

3317197
Considering the fact that they are the evil counterparts of the mane six it's doubtful, plus there's the fact that they still want to kill them.

3317216 Not what I'm getting at. Who's to say that they might not want to have a little bit of fun with the bodies? Try to ruin their lives?

3317221
True that would make for an interesting concept, you considering trying this story out?

3317227 I might. Though we need to get the other one's first chapter out of the way.