Superman has incredible physical abilities that give him a huge advantage at first glance. But Batman is known for his preparation and ability to find solutions to seemingly impossible problems. Naruto's ninjutsu skills are also not to be underestimated. If the fight takes place in a setting where Naruto can manipulate the environment using his earth - style jutsu, he can create obstacles for Superman. Batman could then use his gadgets to further disable Superman. So, it's not clear - cut. If they all fight fair, Superman might have the upper hand, but with teamwork and strategy, Naruto and Batman could potentially take him down.
One possible reason could be mind control. Maybe some villain has taken over Superman's mind and made him do it. Another reason might be a fundamental difference in their ideologies that has escalated to the point of no return.
Lois Lane is often a popular character. In fanfiction, she might play a crucial role in mediating between Batman and Superman or getting involved in their adventures in a more hands - on way, using her investigative journalism skills.
Alfred Pennyworth is quite popular too. He can offer his wisdom and support to Batman, and his interactions with Superman can be both humorous and heartwarming. He's like the glue that holds things together in the Batcave, and his presence can bring a sense of home to the story.