In this fanfiction, their first meeting would be quite something. Naruto, with his bright orange jumpsuit, would stand out in Jessica's gritty world. But once they start talking, they realize they have common goals. Both are used to fighting against the odds. Naruto against powerful ninja foes and Jessica against the seedy underbelly of her city. Their combined skills would allow them to take on threats that neither could handle alone.
Yes, they could be unlikely allies. Naruto's superhuman abilities from being a ninja and Jessica's detective skills and super strength could combine in a unique way. Maybe Naruto needs help finding a missing person in Jessica's world, and she enlists his help because of his tracking skills. Together, they would make a formidable team.