One interesting concept could be the clash of different ideologies. In Warhammer 40k, there is a lot of grimdark and a strict hierarchy, while Star Trek is more about exploration and unity. So seeing how characters from both universes react to the other's values can be really engaging.
Well, the races are very different. In Star Trek, you have the Federation races like Humans, Vulcans, and Klingons. They generally have a more diplomatic approach. In Warhammer 40k, races like the Orks are just out for a good fight all the time. So in a crossover, the Orks might see the Klingons as kindred spirits in a way, but the Klingons would probably be put off by the Orks' lack of honor.
A common crossover is the appearance of Starfleet officers in the Warhammer 40k universe. They might be seen as strange and otherworldly beings. Their peaceful exploration ethos would be a sharp contrast to the constant warfare in 40k. For example, they could try to broker peace between warring factions in 40k, which would be a huge challenge given the nature of that universe.
Sometimes, the interactions are based on a need for mutual assistance. A Star Trek ship might find itself in the Warhammer 40k universe and need the help of a local faction to repair their ship. In return, they offer their knowledge or technology. This can lead to some interesting exchanges as the characters from both universes try to understand each other's values and capabilities.
In Warhammer 40k, the Emperor is an extremely powerful character. His psychic powers are off the charts and he has a huge influence over the entire Imperium. In a face - off against Star Trek characters in fanfiction, he would be a formidable force. In Star Trek, Q is a very powerful being. He can manipulate reality at will. If Q were to engage with the Emperor, it would be a battle of two extremely powerful entities with different natures. Q's mischievous and almost omnipotent nature against the Emperor's more serious and controlling power would be quite a showdown.
The space battles are often the highlight. Warhammer 40k has huge fleets of gothic - looking ships armed with massive guns and torpedoes. Star Trek has its own sleek starships with advanced weaponry like photon torpedoes and phasers. In fanfiction, a large - scale battle between a Warhammer 40k imperial fleet and a Star Trek Federation fleet would be amazing. The different tactics, ship designs, and crew capabilities would all come into play. For instance, the hierarchical and often fanatical nature of the Warhammer 40k crews compared to the more diverse and diplomatic Star Trek crews would lead to very different decision - making processes during the battle.
One interesting plot twist could be the combination of the Force from Star Wars with the psychic powers in Warhammer 40k. Imagine a Jedi using his Force powers in the grim and dark universe of 40k, facing off against Chaos psykers. Another could be the appearance of Imperial Stormtroopers in a Warhammer 40k battle, their white armor standing out among the chaos. Maybe they could be mistaken for some sort of new xenos threat at first. And a third plot twist might be the discovery of a lost Star Wars planet in the Warhammer 40k galaxy, full of unique technology and species that both sides would be eager to control or destroy.
Perhaps an Imperial Inquisitor ends up in the Star Wars galaxy and tries to manipulate the Sith and Jedi for his own ends. He could see the Sith as a useful tool, not realizing how dangerous they truly are until it's almost too late. This could lead to a three - way battle between the Inquisitor, the Sith, and the Jedi.
One great 'Warhammer 40k Emperor Crossover Fanfiction' is the one where the Emperor crosses over into a modern Earth setting. It shows how his powerful psychic abilities and leadership skills shock the modern world.
The Emperor Palpatine and the God - Emperor of Mankind. Both are extremely powerful and have a far - reaching influence over their respective universes. A crossover between them could explore themes of ultimate power, tyranny, and the price of maintaining control over vast empires.