Author's Note

All the events mentioned here happen within their canon episodes. This part gives more context for some of them, going into what happens during them.

Aftermath

Over 1,000 years have passed and the Crystal Empire has finally returned as well as King Sombra. Sombra was starting to ask himself, “What happened? Why did the spell wear off? It was meant to last forever!”

He soon noticed two ponies making their way toward the Crystal Empire. They were Princess Cadance and Shining Armor and they were tasked by Princess Celestia to protect the recently returned kingdom. The dark unicorn king couldn’t remember who the alicorn was but she looked familiar to him. Questions for later.

King Sombra soon appeared behind them in his shadow form and lunged toward them. They ran until they made it to the Crystal Empire. Cadance quickly put up a big shield around the empire, keeping Sombra from ever fully returning to the throne and you know the rest of that tale. Twilight and her friends find the heart, return it to where it belongs, and Sombra is finally destroyed.

The Alicorn Amulet has been moved to many different places over time and has been worn by many different ponies who desired more power, but they were eventually convinced to take it off.

The amulet finally lands in an old shop, where it is then bought by a very jealous unicorn. As she used it, it started to affect her. It began to make her more like Sombra. That is from the corrupted magic Sombra had stolen all those centuries ago.

When the Crystal Heart was shattered by Flurry Heart, it reveals that Sombra had put up another curse on the empire that no pony ever found out about even after everything.

That curse is causing the Arctic North’s wintry weather to be even worse and freeze over everypony in the Crystal Empire once the Crystal Heart is destroyed. He used it as a threat to those who dared to disobey him. This isn’t where his story ends, however.

He is brought back once more by something. He was told about a secret lair that he must go to. Once he arrives, he notices Chrysalis there along with a centaur, Tirek, and a little filly, Cozy Glow. He doesn’t want to look at Chrysalis or even acknowledge her because of her failures all those years ago. Then, the creature that brought him back, walks in and reveals himself to be Grogar.

Grogar wants him, Tirek, Chrysalis, and Cozy Glow to work together so they all can rule Equestria. King Sombra refuses as he wants to be the only ruler of Equestria, wanting to rule it in despair and fear, and he also feels like teamwork like this is a waste of his time.

So he is sent to the Crystal Empire and easily takes back control of it. During his attack, his mind controls the guards and also threatens to kill a baby Alicorn in front of her parents.

As Sombra traps the royal family inside his dark crystals, he then says, “I recognize you now princess. You the little pegasus child to Amore. Oh, I would have loved to make you watch as she perished.”

Twilight and her friends soon arrive with the Elements of Harmony to destroy him once again, but Sombra forces them to endure their worst fears by experiencing them while he leaves them in a state of despair. As he was doing this, he then gained some very interesting information that he will use later. But then, the Mane 6 break free and they blasted Sombra away with the Elements, or that is what they believe. The truth is that it was a faked defeat.

He secretly follows them to the Tree of Harmony, believing it’s the source of their most powerful magic, and then destroys it so the ponies wouldn’t use the Elements on him ever again. He also knew that the Everfree Forest would spread because when he subjects those to their worst fears, he's also capable of seeing through the memories. Using this newfound knowledge, he decides that it would also be fun to have the forest cause destruction alongside him.

He then leaves to mind-control everypony in Ponyville, including the ones that the Mane 6 loved closes, and goes to take revenge on Celestia and Luna. That would be the last thing he would ever try to do as Discord would motivate Twilight and her friends to stand up to him without outside help and they show Sombra how powerful friendship magic truly is. He is then destroyed once and for all.

However, in an alternate timeline, King Sombra does succeed in retaking the Crystal Empire and rages war against Princess Celestia intending to kill her and then take over the entire world, spreading misery and despair to all life. In that timeline, the battle is still going on, with millions dying on either side, and no one knows who will win.