Well, if it's a crossover with the Transformers universe, Optimus Prime could be a main character dealing with the battle droids. He could try to teach them about honor in combat, which is very different from their programmed aggression.
In a crossover with the Mass Effect series, Commander Shepard could be the main character. Shepard would likely view the battle droids as either a potential threat or a useful tool in the fight against the Reapers. The interactions between Shepard's team and the droids would be full of drama and strategic decisions.
A new, self - aware droid created during the crossover event could be the main character. This droid could start out as a regular battle droid but then gain sentience and lead the droid army in a different direction. It could question the purpose of war and try to find a more peaceful solution for the droid army.
For main characters in a 'Star Wars Droid Rebellion' fanfiction, there could be a group of droids. Firstly, an old medical droid that has seen too many droids being deactivated without proper care. It decides to use its knowledge of droid anatomy to help the rebels. Then there's a security droid that has been reprogrammed by accident to have emotions. This security droid uses its combat skills to protect the other rebels. And finally, a droid engineer who creates new weapons and defenses for the droid rebellion, using its skills to turn the odds in the droids' favor.
How about a crossover with the Harry Potter world? The battle droids could be found in Hogwarts. They might be confused by the magic there and the students could try to figure out how to use their technology. And the droids would surely be a strange sight among the wizards and witches.
It could be R2 - D2 and C - 3PO as they are very popular droids in the Star Wars universe.
It's also possible that there are various side characters like the local inhabitants of the places the droid visits. For instance, if the droid travels to an alien planet, there could be friendly or hostile aliens that play important roles in the story, interacting with the droid in different ways and affecting its journey.
Perhaps some of the more mysterious characters from the series could take the lead. For example, Isabel Kabra. Her devious nature could add a whole new layer of intrigue to the crossover fanfiction. She could be working with or against the other characters in unexpected ways, creating a lot of tension and interesting plot twists.
A group of scientists who were involved in creating the Indoraptor in the first place could be main characters. They might have to face the consequences of their creation when it crosses over into another world or situation. They would be trying to either control it or destroy it.
If it's a crossover with the DC universe, Batman could be the main character. He would use his detective skills and arsenal of gadgets to face the Deathclaw. His dark and brooding nature would make for an interesting contrast against the brute force of the Deathclaw.
Definitely, Cortana could be a main character in a 'halo anime crossover fanfiction'. If she were in the world of Code Geass, she could help Lelouch with his strategic plans, using her vast knowledge and intelligence. Another option is the Elites from Halo. They could be the main characters in a crossover with My Hero Academia. Their physical strength and warrior culture could be contrasted with the superheroes in that anime, and they could have some interesting interactions with the students at UA High.
Obviously, Naruto would be one of the main characters. He's the protagonist of the Naruto series and would be the main link to the ninja world in this crossover. Another could be a young Kitsune, maybe one that's just coming of age in the Kitsune world. Their paths cross, and they have to learn to work together.