It could be other students at Hogwarts who sense something strange about Snape and his invisible friend. They might try to expose Snape's secret out of jealousy or because they think it's some sort of dark magic.
Perhaps there is a powerful dark wizard from the past whose spirit is awakened by the presence of Snape's invisible friend. This dark wizard sees the invisible friend as a threat to his own plans for resurrection or domination and tries to destroy it, with Snape caught in the middle.
One idea could be that Snape's invisible friend turns out to be a manifestation of his repressed childhood self. It could help him face his past traumas and insecurities.
A new and original antagonist could be a rogue psychologist who has developed a powerful hypnosis technique. This character might be jealous of Peter's abilities and want to use hypnosis to take over his mind and use his powers for their own gain. Or it could be a secret organization that wants to use Peter as a weapon, and they use hypnosis as a means of control.
Another option is a group of demons who have a vendetta against Clary or the shadowhunters in general. They might use torture as a way to break her spirit and gain information about the shadowhunters' defenses.
The father of the baby could potentially be an antagonist if he has a different view on the pregnancy than Lucy. For example, if he wants her to have an abortion and she wants to keep the baby, he could create obstacles for her.
One possible antagonist could be Orochimaru. He might be interested in Kim's unique skills and gadgets for his own evil experiments. He could set a trap for her and Naruto would have to save her from Orochimaru's clutches. Another could be Drakken. He might team up with some ninja villains, like the Akatsuki members, in order to achieve his own goals. Naruto and Kim would then have to face this combined force.
Well, it could be that in this fanfiction, Snape is written in a way that endangers Harry's friends. Harry is very protective of his friends, so if Snape is portrayed as harming them in some way, Harry would likely try to destroy whatever it is that's causing the threat. Also, it could be related to some prophecy or hidden knowledge in the fanfiction that makes Harry believe Snape has to be stopped.
The hunters could be antagonists. They might see the werewolf boy as a dangerous creature and try to hunt him down.
If Izuku is an alien, the antagonists could be other aliens who want to use his unique powers for their own evil purposes. Maybe they see Izuku as a key to conquering Earth or other planets.
Perhaps there could be an organization that wants to control the Yu - Gi - Oh world. They view the Queen of Games as a wild card that could disrupt their plans. So they send their own powerful players to stop her. They might use underhanded tactics like cheating or sabotaging her decks. This would create a lot of conflict and drama in the fanfiction.
Well, perhaps the Invisible Woman is actually a cursed being in the Naruto world. She was once a normal ninja but due to a forbidden jutsu, she became invisible. Naruto and his team take it upon themselves to find a way to reverse the curse. As they journey together, they face many challenges and also discover secrets about the origin of the jutsu that cursed her. In the process, the Invisible Woman also helps them in battles with her unique abilities.