How about a crossover with 'Final Fantasy'? The different job classes in Final Fantasy could be compared to the various character types in Warhammer Fantasy. For instance, the Black Mages in Final Fantasy could team up with the Warhammer Fantasy mages to cast powerful spells against a great evil. And the idea of having Warhammer Fantasy's Chaos forces corrupt some of the beautiful and idyllic worlds in Final Fantasy could create a really dark and engaging story.
One idea could be a crossover with Star Wars. Imagine the Imperium of Man encountering the Galactic Empire. The two totalitarian regimes could have some intense ideological battles and epic space battles as well.
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.
One idea could be a crossover between Warhammer and Lord of the Rings. Imagine the Space Marines facing off against the Orcs of Mordor. Another could be a Warhammer and Star Wars crossover, like the Imperium of Man encountering the Galactic Empire. Or perhaps a crossover with the Witcher, where Witchers team up with Warhammer's warriors to fight common foes.
One idea could be the Imperium of Man encountering the Citadel Council. The Imperium's strict dogma and military might would clash with the Council's more diplomatic approach. For example, the Space Marines might be seen as terrifying super - soldiers by the Mass Effect races.
One idea could be to combine the unique weaponry of RWBY with the grimdark setting of Warhammer. For example, Ruby's scythe could be enchanted with some sort of Warhammer - style magic or runes. Another idea is to have the characters from RWBY face off against Warhammer - style daemons or chaos warriors. This would really test their skills and teamwork. Also, the concept of semblances could be related to the powers in the Warhammer universe in some way, like a character's semblance being a form of psychic power in the context of Warhammer.
One idea could be to have the Lizardmen cross over with a modern-day military unit. The contrast between the primitive - yet highly advanced in their own way - Lizardmen and modern military technology would create interesting scenarios. For example, how would the Lizardmen react to firearms? Another could be a crossover with a fantasy world like Middle - earth. The Lizardmen's unique culture and magic could interact in fascinating ways with the races and magic of Middle - earth.
One interesting concept could be a 'Warhammer' crossover with 'Lord of the Rings'. Imagine the orcs from 'Warhammer' interacting with the orcs from Middle - earth. Another could be a crossover with 'Star Wars', like the Space Marines teaming up with the Jedi or Sith in some strange alternate universe scenario. And a 'Warhammer' and 'Harry Potter' crossover where the magic of the wizarding world meets the dark and gritty world of 'Warhammer' would also be really cool.
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 crossover with the Star Trek universe. The Tyranids could be seen as an extremely hostile alien force that the Federation has to deal with. Their bio - ships and swarming tactics would be a huge contrast to the more technological - based Starfleet.
One idea could be a story where a character from one Total War Warhammer faction gets transported to another faction's territory and has to adapt to survive. For example, a High Elf finding themselves in the midst of a Greenskin horde. They would have to use their wits and combat skills in a very different environment.