There could also be a powerful magical creature that has been corrupted by dark magic. This creature might be feared by all in the past, and when Harry arrives, it sees him as a new target or a potential source of power. Harry has to figure out how to defeat it using his own skills and the limited resources available in the past.
Perhaps it's a dark spirit that has been trapped in the Acrobleno for centuries. When Harry arrives, it senses his power and wants to possess him or use his magic for its own evil purposes. So it becomes the main antagonist, constantly trying to harm Harry and stop him from leaving.
One idea could be Harry using his modern magic knowledge to shock the wizards of the past. For example, he might introduce spells that were lost over time.
It could be a new Death Eater in disguise who has infiltrated Hogwarts under a false identity. They could be causing trouble by secretly spreading dark magic among the students.
The main antagonist could be a powerful necromancer who combines the dark arts of Skyrim with some elements of Voldemort - like magic. He could be raising an army of the undead and causing chaos across Skyrim, which Harry has to stop.
It could be a new dark wizard who has a vendetta against Harry. This wizard might use a spell to stop Harry from eating, thinking it will weaken him before a final showdown. He could be someone who was once a follower of Voldemort and now wants to take his place and prove himself by getting rid of Harry.
Maybe an ancient evil spirit that was once bound but is now trying to break free by using the summoner as a conduit. This spirit could be manipulating events from the shadows, causing chaos in the wizarding world to draw the summoner out.
It could be an ancient and powerful Titan who was thought to be defeated long ago. Since Percy is in the past, this Titan could be in his prime and see Percy as a threat to his plans of ruling over the world again. For example, Kronos might be even more powerful in this past era and Percy has to find a way to stop him without the help of his modern - day friends.
The main antagonist could be a rogue ninja who has infiltrated the village's council. This ninja could be secretly manipulating things behind the scenes to get Naruto sent to prison. He might have a vendetta against Naruto for some past encounter or just see him as a threat to his own evil plans.
Perhaps one of the Titans who were banished to Tartarus. They might see Percy as a threat to their plans of revenge or escape. Kronos, if he still has some form of existence in Tartarus, could be a major antagonist. He would have his own motives and powers, and he could try to manipulate Percy or simply get rid of him.
Perhaps an ancient spirit that has been awakened by the imbalance in the life - death cycle due to Harry becoming the Master of Death. This spirit sees Harry as the cause of the chaos and tries to destroy him to restore the balance in a way that is harmful to the wizarding world.