There's also a chance that it's a powerful dark spirit that has possessed one of the students or staff members. This possessed individual then tries to harm Harry, getting him to the brink of death. The spirit could be using the person's body to get closer to Harry without raising suspicion.
Perhaps it's an older student who has been corrupted by dark magic. They might be jealous of Harry's fame and power, and so they plot his death. They could use their knowledge of the castle's secrets to put Harry in life - threatening situations.
It could be a new dark wizard who has infiltrated Hogwarts under the guise of a new teacher. This wizard might have a vendetta against Harry specifically and sets up elaborate traps to kill him.
One scenario could be that he is poisoned by a mysterious potion slipped into his food in the Great Hall. Maybe a Death Eater sympathizer among the students manages to do this.
Most likely, Voldemort would remain the main villain. Without Harry to stop him, he would be free to carry out his evil plans unopposed.
Maybe Dumbledore. He is extremely powerful and has a great deal of knowledge about dementors. He could arrive just in time, using some mysterious and powerful magic that we haven't seen before to rescue Harry. His presence would also add an element of mentorship and guidance as the story progresses.
It could be an unknown, ancient evil that has been awakened. This villain might have powers far beyond what Naruto and Sasuke have faced before. Maybe it's an entity from a forgotten era that was sealed away long ago and now has broken free.
It could be a new character entirely. Maybe a rogue ninja from a long - forgotten clan who holds a grudge against Naruto for some past event. This villain could be extremely powerful in dark jutsu and sees Naruto's death as the first step in his plan to take over the ninja world.
It could be Doctor Doom. He might be seeking to take over multiple universes in a crossover. Spider Man stands in his way, and Doom, with his superior intellect and powerful magic, manages to defeat Spider Man. His death would then be a huge shock to other heroes in the crossover, like the Avengers or the Fantastic Four who then have to avenge him.
Voldemort is often involved. Since he's Harry's main enemy, he might set up elaborate plans to kill Harry. For instance, he could use a powerful artifact to lure Harry into a deadly situation.
Voldemort would surely be a main character. With Harry dead as a baby, Voldemort's actions and how he further consolidates his power would be a major part of the story.
It could be a new dark wizard who has been secretly plotting in the shadows. This wizard might be jealous of Harry's fame and power, and decides to make him disappear so that he can rise to power unopposed. He could have a group of followers who are experts in dark magic and are able to carry out his plan to make Harry vanish.
The Queen of Hearts would make a great main villain. Her tyrannical rule and quick temper in the original Wonderland story could be amplified in a fanfiction. She could be a powerful dark magic user who sees Harry as a threat to her rule and tries to stop him from achieving his goals in Wonderland.