A plot could revolve around a Dark Elf sorceress who discovers a powerful and ancient magic that was lost. But this discovery attracts the envy and wrath of other powerful Dark Elves. She has to fight for her life and the right to keep this magic while also using it to her advantage in the cut - throat Dark Elf hierarchy.
A plot could involve a dark elf noble trying to gain more power within the dark elf society through political intrigue and backstabbing. Or it could be about a dark elf warrior who has a change of heart and tries to break away from the cruel ways of his people. There could also be a fanfiction where dark elves team up with other races, like the skaven, for a common goal, but with their own hidden motives.
Perhaps a Dark Eldar wych could form an unlikely alliance with a Space Marine. Maybe the wych has a personal vendetta against a chaos warband that is also targeting the Space Marine's chapter, and they decide to work together to take down the common enemy. This would involve a lot of tense moments as they try to trust each other despite their very different cultures and motives.
One idea could be that the Dark Elves are searching for a powerful energy source that exists in the 'Worm' world. This draws the attention of both the 'Worm' capes and a Marvel hero, like Iron Man. Iron Man is intrigued by the technology in the 'Worm' world and teams up with some of the local capes to stop the Dark Elves from getting the energy source. Another plot could involve a 'Worm' character with the power to teleport being accidentally transported to the realm of the Dark Elves. There, they meet a Marvel villain who has also ended up there. They must then work together to find a way back to their respective worlds while dealing with the Dark Elves.
Then there's Lelith Hesperax. Her skills as a fighter and her status within the Dark Elf society can be used to create exciting stories. Fanfiction might focus on her battles, her rivalries, or her attempts to gain more power and influence among the Dark Elves.
Another plot could be a crossover where the Skaven meet a group of powerful mages from another universe. The Skaven, being cunning, would initially try to deceive the mages and use them for their own gain. But as the story progresses, they find out that the mages are not so easily fooled and a battle of wits and magic ensues.
One idea could be a vampire Space Marine. Maybe a genetic experiment gone wrong in the Imperium that results in a Marine with vampiric traits. He has to struggle with his newfound thirst while still trying to fulfill his duty to the Emperor.
Maybe a plot where a group of Warhammer heroes are sent to the Hero Academia world to stop a chaos invasion that is starting to seep into that realm. They have to work with the local heroes, sharing their knowledge of dark magic and ancient weapons to combat the new threat. This would involve a lot of cultural clashes and learning experiences between the two groups.
A cool plot for Warhammer Fantasy Crossover Fanfiction could be a crossover with the Final Fantasy series. Picture a Warhammer elf meeting a Final Fantasy summoner. They could exchange knowledge about different magical creatures. Also, a crossover with the Naruto universe would be interesting. A Warhammer Chaos warrior might find himself in the Hidden Leaf Village and cause chaos (literally) among the ninja. Or, a crossover with the Witcher world. Geralt could team up with a Warhammer Witch Hunter to hunt down monsters that are a threat to both their worlds.
A plot could involve the forces of Warhammer trying to harness the power of the Doom Slayer. They see his incredible combat abilities and want to use him in their battles. However, the Slayer has his own mission and is not easily swayed, leading to a conflict of interests and some intense battles.
One idea could be that Naruto characters are transported to the Warhammer universe. For example, Naruto himself could be mistaken for a powerful chaos warrior due to his chakra. He might then have to prove that he's not a threat while also trying to find a way back home. Another plot could involve the shinobi clans of Naruto being compared to the different factions in Warhammer. The Uchiha with their Sharingan could be seen as having a similar level of mystery and power as some of the Warhammer sorcerers.