The main villain could be a group of Slytherin students led by someone like Draco Malfoy. In this fanfiction, they could be more extreme in their pure - blood beliefs and see Harry as a threat to their way of life. They could plot and succeed in killing Harry during his first year, perhaps with the help of some dark magic artifacts or spells that they manage to get their hands on.
Quirrell could be the main villain. He was already under Voldemort's influence in the original story. It's possible that in this fanfiction, he doesn't hold back and attacks Harry more directly and lethally during his first year. Maybe he uses his position as a teacher to get close to Harry and then strikes when he has the chance.
It could also be a dark wizard from the past who has been trapped in a hidden part of Hogwarts and is now released during Harry's third year. This wizard could have a vendetta against the Potter family or Gryffindor house and start causing trouble.
In that fanfiction, it could be that a character who was secretly working for Voldemort, perhaps someone we didn't suspect at first, like a seemingly innocent teacher or a student who was under the Imperius Curse. Another option is that a group of dark wizards invaded Hogwarts and Harry was unfortunately caught in the crossfire and killed. Or perhaps a magical artifact malfunctioned and ended up being the cause of his death.
One possible plotline could be that the troll in the bathroom attacks Harry more brutally and he succumbs to his injuries. Another could be that Quirrell, being a servant of Voldemort even earlier, manages to directly attack Harry and kill him before he has a chance to figure out what's going on. Maybe there's a dark wizard who infiltrates Hogwarts on the very first day and targets Harry specifically, seeing him as a threat even at that young age.
A new dark wizard or witch could be the villain. Maybe they are jealous of Harry's fame and power. They study dark arts intensively and develop a spell to trap Harry in his mind. This new villain might not be directly related to Voldemort but has their own evil motives, like ruling the wizarding world by getting rid of Harry who is seen as a major obstacle.
It could be a new character created by the fanfiction author. Maybe a powerful wizard who was once shunned by the wizarding community and now wants revenge by stealing magic.
A dark wizard who has merged the dark arts with Wonderland's magic could be the main villain. He might have created some sort of dark Wonderland where all the creatures are under his control, and Harry has to break this control to restore balance.
It could be a rogue wizard who was once a student at Hogwarts and has a vendetta against the school. He was expelled for practicing dark magic and now he's back to cause trouble. Maybe he wants to steal some powerful magical artifacts from the school's vaults.
Perhaps the main villain is actually a corrupted version of a well - known character. For example, if Hermione was somehow influenced by the dark magic associated with the runestone path and turned against Harry. It would be a very unexpected and heart - wrenching twist, as she has always been such a loyal friend. But the power of the runestone path could be so strong that it changes her fundamental nature.
Maybe a new character, a Muggle - born wizard who was shunned by both the Muggle and wizarding worlds. This character, out of bitterness, decides to combine Muggle technology and magic to create the droid army and rule over both worlds. He would see Harry Potter and his friends as the main obstacles to his grand plan.
It could be someone new, a dark wizard who has learned about Naruto's reincarnation and wants to use his power for evil. This new villain might try to manipulate Naruto into using his chakra in a wrong way. Or perhaps it could be a combination of Voldemort and some of Naruto's old enemies from his previous life who somehow find a way to merge their powers in the Harry Potter world.