Another possibility is a group of rogue mages who oppose the way magic is being taught and regulated. They target Callum Hunt because he is seen as a symbol of the establishment. Their attacks on him could eventually lead to his death in the fanfic.
It could be an ancient dark wizard who has been resurrected and sees Callum Hunt as a threat to his plans of world domination. This wizard could use his powerful dark magic to overpower Callum and ultimately cause his death.
Perhaps in the fanfic, Callum Hunt is poisoned by an enemy who has infiltrated his inner circle. Despite his friends' efforts to find a cure, he succumbs to the poison, and his death leads to a series of events where his friends vow to avenge him and make the magical world a safer place.
A rogue ninja from another village could be the main antagonist. Maybe a ninja from the Hidden Mist Village who has a personal grudge against Konoha and sees Naruto as the symbol of Konoha's strength. So, he devises a complex plan to take down Naruto. This ninja could have some unique and deadly jutsu that Naruto has never faced before, which ultimately leads to his downfall.
It could be a powerful sorcerer who wants to take over Crookshnks' homeland. This sorcerer has dark magic and sees Crookshnks as a threat to his plans, so he devises a scheme to eliminate him.
A new organization that is bent on world domination could be the main antagonist. They set a trap during Naruto's mission. This organization might have access to some ancient and forbidden jutsu that they use against Naruto. They see Naruto as a major threat to their plans, so they target him specifically.
It could be a rogue ninja who was secretly plotting against Naruto all along. After Naruto's death, this antagonist could emerge and try to take over the village, seeing it as the perfect opportunity with the village in mourning and a bit disorganized. This ninja might have some personal vendetta against Naruto and now wants to make the village pay.
An alien race with a grudge against the Republic could also be the main antagonist. They might target Rex specifically because of his strategic importance and his role in leading many successful missions against them in the past. His death at their hands would be a major blow to the Republic's morale.
It could be a rival family who had some sort of long - standing feud with Sakura's family. They might have caused their deaths in an underhanded way and now Sakura has to deal with them as she tries to uncover the truth.
A powerful crime lord could be the main antagonist. If Castle's father was getting too close to uncovering their illegal activities, they might have made him disappear. Now that Castle is hunting for his father, they try to stop him by any means necessary, sending their henchmen after him and trying to mislead him with false information.
A powerful and corrupted nymph could be the main antagonist. She was once a friend to the Hunt but was lured to the dark side by some ancient magic. Now she wants to destroy the Hunt and take over their territory. She uses her powers over nature to create all sorts of obstacles for the Hunt and Percy, if he's involved. She could also be very manipulative, turning some of the Hunt members against each other.
Hawkmoth could be the main antagonist. In the original story, he's always causing trouble. In a 'marinette dies' fanfic, he could finally succeed in his evil plan, maybe by getting his hands on the Ladybug and Cat Miraculouses and using their combined power against Marinette.