Maybe some anti - Muggle - born wizards could be the antagonists. They don't want Harry, the son of a Muggle - born mother, to enter Hogwarts. They could try to stop Snape from delivering the letter, creating a struggle for Snape who has to deal with both his own prejudices and his duty.
It could be Voldemort. Even though he doesn't directly appear in the act of letter - delivering, his influence might be hovering over Snape. Snape might be worried that by delivering the letter, he's bringing another potential threat to Voldemort, and Voldemort's shadowy presence could create conflict for Snape.
Maybe Snape has some complex emotions while delivering the letter. He might be secretly hoping Harry won't come to Hogwarts because of his dislike for James Potter, yet he has to follow Dumbledore's instructions.
Well, in this fanfiction, Snape might be forced by some magical circumstances to deliver Harry's letter. Maybe Dumbledore has a secret plan and Snape is reluctantly following it. It could lead to some interesting interactions between Snape and Harry, perhaps Snape finally shows a bit of kindness that Harry never expected from him.
Dumbledore could be involved. He often has his fingers in many pies at Hogwarts, so he might be the one who arranges for Snape to deliver the letter to Harry for some greater good or part of his grand plan. Another possible character could be Hermione. She might notice something strange about Snape delivering the letter and start to investigate, suspecting that there's more to it than meets the eye.
The letter might be a summons to a secret wizarding council. Harry Snape's journey to deliver it could involve him facing his own inner demons as well as external obstacles. He might have to pass through dangerous terrains and encounter magical beings that are either trying to stop him or help him depending on their own agendas. As he gets closer to his destination, he discovers more about the true nature of the council and his role in the wizarding world.
The main antagonist could be an ancient evil spirit that has been awakened by the mixing of ninja and wizarding magic. This spirit is angry at the intrusion and starts to possess students and teachers at Hogwarts. The ninja and Harry Potter must figure out how to exorcise the spirit before it's too late and Hogwarts is completely taken over.
It could be a new dark wizard who is jealous of Harry's new mastery. This wizard might try to steal Harry's knowledge or use it for his own evil purposes. He could be a former Death Eater who was thought to be dead but has now returned with a vengeance.
It could be a new dark wizard who has been lurking in the shadows. Maybe someone who was once a student at Hogwarts but turned to the dark side.
Perhaps a group of rogue Hogwarts students who have fallen under the influence of dark magic. They want to use Harry for some dark ritual, and Snape becomes an unexpected shield for Harry. Snape has to deal with the internal problem of the school while also protecting Harry from these students.
A dark wizard or witch from outside Hogwarts could be the main antagonist. They might target Harry specifically because of his reputation as the 'Chosen One' and use their influence to get him expelled from Hogwarts so that he is more vulnerable and easier to attack.
The main antagonist could be an old, corrupt house - elf. This house - elf was mistreated in the past at Hogwarts and has now turned to the dark side. It wants to bring chaos to Hogwarts and sees Lady Hogwarts as the key. It uses its knowledge of the school's hidden passages and secrets to plot against her. Harry Potter, being the defender of the underdog, tries to reason with the house - elf at first but when that fails, he has to use magic to stop it from harming Lady Hogwarts.