The Arbiter is another great character. His complex backstory and his position within the Covenant can add a lot of depth to a fanfiction. He might be the one trying to convince his own people to ally with the humans.
Cortana could also be a key character. Her intelligence and relationship with Master Chief can be explored further in the context of the alliance. Maybe she could be the one to figure out a way to communicate effectively between the humans and the Covenant.
Often, the Master Chief is a popular character to include. His combat skills and leadership make him a great addition to any story involving a human - elite alliance. He can represent the best of humanity in the face of a new partnership with the elites.
Master Chief is definitely one of the most popular. He's the face of the Halo series, so fans love to see him in crossovers. Cortana is also a popular choice. Her complex character and her relationship with Master Chief make for interesting crossovers. The Arbiter is another character that often features. His unique backstory and his role in the Halo universe can add a lot to a crossover story.
One idea could be a story where a group of humans and Covenant members are forced to team up against a new, greater threat that endangers both their species. Maybe a powerful alien race that neither has encountered before.
Often, the Spartan soldiers are very popular characters in Halo Human Empire fanfiction. Their super -human abilities and military training make them natural heroes in many stories. They can be portrayed as lone warriors or leaders of military campaigns against the Covenant or other threats.
In Halo Warhammer 40k crossover fanfiction, the Librarians from Warhammer 40k are quite popular. Their psychic powers can lead to some really cool interactions with Halo's technology and characters. They can sense things in the Warp, and how would that work when dealing with the more scientific Halo universe? Cortana from Halo is also a favorite. Her artificial intelligence is something that doesn't really exist in the same way in Warhammer 40k. So seeing her interact with the various tech - priests or even daemon - possessed entities could be really interesting. Additionally, Chaos Space Marines are often used for their menacing and unpredictable nature in crossovers.
Sasuke is also a favorite. His complex personality and his journey of redemption or further descent into darkness, depending on the fanfiction, can be really engaging. Writers can play with his relationship with other characters, especially Naruto, in many different ways.
Master Chief from Halo is often a popular choice. His badass, no - nonsense attitude and his combat skills make him a great character to put up against the Jedi or Sith in Star Wars. In Star Wars, Darth Vader is also a very popular character to include. His iconic look and his powerful Force abilities can create some really intense scenes when pitted against Halo characters.
One character that is often used is Cortana from Halo. Her intelligence and relationship with Master Chief can be a great addition to a crossover. In the Starcraft universe, she could interact with the AI units there. Then there's Fenix from Starcraft. His honor - bound nature and combat prowess would be cool to see in the Halo setting. Also, the Flood-infected characters in Halo could be a unique addition to a Starcraft crossover. They could pose a new kind of threat to the Starcraft races, and seeing how the different factions deal with them would be engaging.
The Master Chief is also a common character. His stoic nature and incredible combat skills can create interesting dynamics when paired with an elite character. In some fanfictions, he might be forced to work with an elite against a common enemy much stronger than either of them alone.
Definitely Master Chief. His stoic nature and combat skills would be really interesting to pair with Pokemon. He could be a silent but effective Pokemon trainer. Another would be Cortana. Her intelligence could be used to analyze Pokemon abilities and strategies. And of course, Pikachu would be a great character to include. It could be fun to see how it interacts with the Halo characters and technology.