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 magical creatures could be the main antagonists. They might be angry about how wizards have treated them in the past and decide to take revenge on Hogwarts. They could be led by a powerful and intelligent creature that has a vendetta against the school. In this fanfiction, they could be causing chaos and destruction, and Harry has to figure out a way to stop them.
There's a chance that a corrupt Hogwarts official or a teacher with a hidden agenda could be the main antagonist. They could be secretly working with dark forces or trying to gain power within the school for their own selfish reasons. They might be manipulating students and events to achieve their goals, and Harry, being the hero, would eventually expose their true nature and put an end to their evil plans.
Maybe it could be a new character who is a combination of ninja and wizardry evils. This character could be jealous of Naruto's unique abilities that bridge the gap between two different worlds and wants to stop Naruto from uniting the ninja and wizarding communities against him. They could have powers that are a mix of dark magic and some dark ninja jutsus.
Well, perhaps in 'harry goes to hogwarts later fanfiction', he could form new friendships. He might meet students from different backgrounds or even different magical cultures, which would bring a whole new dynamic to his Hogwarts experience. He could also discover new magical abilities or spells that were previously unknown to him, which would help him in his adventures at Hogwarts.
It could be a dark wizard who has infiltrated Hogwarts under a disguise. Percy might be the one to first suspect this wizard's true identity.
It could be Voldemort if the story takes place during the time he was a threat. Naruto's arrival might disrupt his plans in some way, so he would see Naruto as an obstacle.
There might be a character who is secretly from the wizarding world but has turned to the dark side. This character could be after Harry in the Ouran setting, trying to use the chaos of the new environment to their advantage to get to Harry without being noticed by the Hogwarts professors.
It could be a new dark wizard that we haven't seen in the original series. This wizard might be jealous of Harry's fame and power and wants to eliminate him by making him disappear.
A jealous classmate could be the main antagonist. This person might be envious of Harry's popularity or the strange things that seem to always work out for him. They could start spreading rumors or trying to trip him up in his studies.
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.
The main antagonists could be those who don't want Harry to receive a proper Hogwarts education. Maybe some dark wizards who fear that Harry will become too powerful if he goes through the Hogwarts training. So, they plot to keep him away from Hogwarts.