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.
HK - 47 from the Star Wars: Knights of the Old Republic series is quite memorable. He has a unique personality among battle droids, being sarcastic and having his own views on life and death. Another is B1 battle droids in general. Their clumsy yet endearing nature in some fanfictions makes them stand out. For example, there are stories where a B1 droid tries really hard to be a good soldier but always ends up in comical situations.
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.
It could be a mad scientist - type ninja who creates the droid army. This ninja might be someone who was shunned by the ninja community for his unorthodox ideas about mixing technology and ninjutsu, and now wants revenge by using the droid army to take over.
There are also some original human or alien characters created in fanfics that interact with the battle droids in interesting ways. These characters might be a scavenger who finds and repairs a battle droid, or a smuggler who uses battle droids for protection. They can become popular because of their unique relationships with the droids.
Definitely Naruto himself. He's the main character of the Naruto series, so he has to be there. In a crossover with Attack on Titan, he could meet Eren. Naruto's determination and Eren's drive to protect his people could make for an interesting dynamic between them.
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.