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.
One interesting concept is the crossover with other popular sci - fi universes. For example, a crossover with Star Wars could have the Imperium of Man facing off against the Galactic Empire. Another concept could be the combination of different Warhammer 40k factions in unexpected ways within the fanfiction. Maybe the Space Marines teaming up with the Orks against a greater threat.
One interesting plot could be Naruto's ninja skills being used in the grimdark universe of Warhammer 40k. For example, his shadow clone jutsu could be a great asset in battles against the various alien threats in 40k. He could create hordes of clones to overwhelm the enemy forces like the Tyranids or Orks. Also, his ability to sense chakra might be similar to the psykers' ability to sense the warp, which could lead to some unique interactions with the Imperium's psykers or the Chaos sorcerers.
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.
Some interesting concepts are the different power sources. In Halo, we have things like plasma and fusion power, while Warhammer 40k has the Warp and its associated powers. How would these interact? Maybe a UNSC ship powered by a fusion reactor has to deal with the unpredictable effects of the Warp when it enters a region influenced by it. And then there's the concept of heroism. Spartans are known for their individual heroics, while in Warhammer 40k, heroism often comes with a heavy price and a lot of religious and ideological baggage. Combining these two views of heroism can make for some thought - provoking stories.
Ruby Rose is often a popular crossover character. Her combat skills and leadership in RWBY make her a natural fit to be inserted into the Warhammer 40K universe. She could potentially lead a squad of Space Marines or be a key figure in a resistance against some of the darker forces. Another popular one is Yang Xiao Long. Her strength and brawler - like combat style can be really interesting when pitted against the various foes in 40K.
The gods in Warhammer 40k are on a whole different level of power. They can warp reality on a galactic scale. In Marvel, the Asgardian gods like Thor have great power, but it's not on the same scale as the Chaos Gods in Warhammer 40k. But if Thor were to face off against a daemon from Warhammer 40k, his lightning and strength might be enough to hold his own, especially if he had the help of some of his Marvel comrades and the technology and weaponry from Warhammer 40k.
You can start by looking on popular fanfiction websites like Archive of Our Own. There are often tags related to 'Warhammer 40k' and 'crossover' which can help you narrow down your search for Emperor - related crossovers.
The Space Marines are often popular. Their super - human abilities and cool armor make them great for crossovers. They can be paired with characters from other universes and show off their combat prowess. Another popular character is Abaddon the Despoiler. His menacing presence and leadership in the Chaos forces can create some intense crossover storylines.
Some interesting concepts include the combination of the different power systems. In Halo, you have the MJOLNIR armor with its energy shields, and in Warhammer 40k, there are psykers with their psychic powers. Imagine a scenario where a Spartan with MJOLNIR armor has to face a Warhammer 40k psyker. How would their powers interact? Another concept is the cultural exchange between the two universes. The military hierarchies and honor codes in both settings could lead to some really complex and engaging storylines when combined.