After successfully murdering king Sombra, the ponies were glad to be able to go back home to Ponyville. It wasn't a very long adventure, in fact it was quite short as far as adventures go, but it was tiring all the same. Applejack returned to the farm to continue with her life, but it was apparent to everypony that she had changed. She had that look in her eyes, the look of somepony who had seen death. Likely because she shot Sombra's face off with a gun. She never told anypony about that, though, and the rest of the group agreed to keep quiet about it as well.
A few weeks after getting home, she ran into Bon-bon in town and they got into another argument. Sadly, Derpy wasn't there to distract them this time, and it broke out into a fight. Despite Applejack's superior muscle mass, Bon-bon simply had too much earth pony magic, and the fight didn't end well for her. After having both of her back legs broken, Applejack was hospitalized. Sadly, she would never make a full recovery.
It was with a heavy heart that the rest of the Apple family decided that they had to put her down. What purpose does a workpony have if it can't work? Everypony is Ponyville attended her funeral, and the element of loyalty was passed down to her daughter, Applebloom.
A few days after Applejack was injured, the Ponyvillians formed a lynch mob and went after Bon-bon for her heretic ways. Speaking ill of the God princess Celestia was punishable by death, and they publicly hung her before tossing her into an unmarked grave.
Lyra, disheartened by the death of her only friend, Bon-bon, took up drinking to try to forget her sorrows. Her depression only grew, though, and she eventually lost her house and job. Finally, she decided that she couldn't even look at Ponyville anymore, and she left for parts unknown.
Derpy came home only to find that her daughter had been taken by the child protection program and placed in a foster home. What's more, she was charged with negligence and was imprisoned for several years as well as fined, as Equestrian law isn't lenient when it comes to children. When she was finally released, she tried to rebuild her life, managing to get a job as a waiter in Manehattan. Unfortunately, much like Lyra, she battled constant depression, and about five months after her release from prison she was found dead in her apartment, overdosed on pain medication. Officially, the police labeled it an accident, but everyone who knew her thought differently.
In the group's hasty exit from Sombra's house after killing him, they forgot something very important. Berry Punch was still gagged and tied on the floor. Sadly, no one realized she was missing until it was too late.
Vinyl Scratch went back to her life among the flesh beasts. Nothing had changed for her, she'd seen death countless times in her seemingly eternal life and she considered the lives of these ponies insignificant. She continued to blend in, biding her time until the opportunity presented itself to strike.
Nothing changed for princess Celestia. She was still a stuck up asshole like before. She felt great joy in trolling her little ponies. Especially Twilight. Celestia's long legs continued to grow, and after a few hundred years the spindly things finally snapped under the weight of her massive ego. She died in a pool of her own blood.
With her sister no longer able to contest her, Luna was finally able to plunge Equestria into eternal night. There were no survivors...
And they all lived happily ever after. The end.