One idea could be that Twilight discovers a way to redeem King Sombra. She uses her magic and knowledge to break through his dark exterior and find the good within him. Maybe she uncovers a tragic past that led him to become so evil.
Another plot could involve King Sombra coming back in a different form, not fully evil this time. Twilight has to figure out if she can trust him. They could team up to face a new, greater threat to Equestria together. Twilight would be hesitant at first but then realizes his new form might be sincere in wanting to help.
One plot idea could be that Twilight has to enter the realm where King Sombra was banished to retrieve a powerful magic artifact. Along the way, she discovers secrets about Sombra's past that make her question if he was truly all evil. Another could be a time - travel plot where Twilight goes back in time and has to prevent King Sombra from ever rising to power in the first place. Maybe she teams up with an ancestor of one of her friends.
A common theme is the battle between good and evil. Twilight represents good with her magic and kind heart, while King Sombra is the embodiment of evil. Another theme is the power struggle. Twilight's magic power is often pitted against King Sombra's dark powers. For example, in many fanfictions, they have magical duels to determine the fate of Equestria.
Well, a plot could be that King Sombra is resurrected by some dark magic, but this time he has a different goal. Instead of just ruling Equestria through fear, he wants to find a way to break the cycle of hatred. He starts to interact with the ponies in a strange way, and they are both scared and intrigued. There could be a pony who tries to understand him and change his view of the world.
One popular 'My Little Pony King Sombra and Twilight' fanfiction is 'The Battle Against Darkness'. It shows an intense encounter between Twilight and King Sombra where Twilight uses her magic to try and stop Sombra's evil plans. Another one could be 'Twilight's Encounter with King Sombra's Legacy' which delves into how Twilight deals with the remnants of Sombra's power even after his defeat.
Their relationship could start off as one of pure enmity. Twilight would see King Sombra as a great threat to Equestria. But as the story progresses, if they were forced to interact more, Twilight might start to see some small glimmers of humanity (or pony - ity) in Sombra. For example, she might notice that he has a love for a certain kind of magic that is not entirely evil.
A fanfiction could focus on how the ponies form an unlikely alliance with some of the Storm King's minions. They realize that they also don't like the Storm King's tyrannical ways and decide to work together to overthrow him. This would involve a lot of character development for both the ponies and the minions.
The relationship could start with hostility. King Sombra being the dark entity he is, would see Twilight as a threat. But as Twilight tries to understand his motives, she could start to chip away at his cold exterior. For example, by showing him acts of kindness and mercy that he may not have experienced before.
One common theme is redemption. Given Sombra's dark nature, many fanfictions explore Twilight's attempts to bring out the good in him. Another theme could be the power struggle. Twilight's magic of friendship against Sombra's dark magic.
Celestia is often paired with King Sombra. Their power levels are somewhat similar, and they represent opposite sides of good and evil, so it makes for an interesting dynamic. Twilight Sparkle is also a common character to be paired with him. Given Twilight's knowledge of magic, she could either be in a battle of wits with Sombra or trying to understand his magic for some reason.
There are some interesting fanfictions out there. One popular one might be found on major fanfiction platforms. You can search by the tags 'My Little Pony', 'Twilight', and 'Sombra'. It often features unique storylines where they interact in various ways, like facing a common enemy or going on an adventure together.