It could also be a new villain who has somehow managed to hack into the Winter Soldier's programming and redirect his mission towards kidnapping Tony. This villain might be someone who wants to create chaos between the Avengers by pitting the Winter Soldier against Tony. They stay in the shadows, pulling the strings while the Winter Soldier and Tony are caught in the middle.
One possible plot could be that the Winter Soldier is under some mind control still and is made to believe Tony is a threat to a certain organization. So, he kidnaps Tony to bring him to his handlers. But during the journey, some of the Winter Soldier's old memories start to surface, which makes him question his mission.
Another possibility is a new villain who has the power to control Bucky's actions. This villain could be after Tony for his wealth or his influence in the superhero community. The villain forces Bucky to do the dirty work while staying in the shadows.
It could be another dark guild. They might be using Gray as a pawn to kidnap Lucy, perhaps because they know of her celestial spirit magic and want to use it for their own evil purposes. Gray may not be fully aware of their manipulation.
It could be Aizawa himself if he's being controlled by something or has some sort of ulterior motive that is not in Izuku's best interest. But if not Aizawa, then there could be a hidden villain who is manipulating Aizawa to kidnap Izuku.
It could be a new, powerful dark wizard who has a grudge against Fairy Tail. This wizard might manipulate Natsu into kidnapping Lucy to create chaos within the guild. The dark wizard could be after some powerful magic that only Lucy can access, and by kidnapping her, they hope to force her to give it up.
Well, Vegeta himself could be seen as the antagonist in the beginning. Since he is the one doing the kidnapping, he's causing distress to Bulma. However, as the story progresses, the real antagonist could turn out to be someone else. For example, another alien race that is after Vegeta and uses Bulma as bait to lure him into a trap. So, it's not so straightforward in a fanfiction.
It could be Orochimaru. He might have manipulated Kushina into kidnapping Naruto. Orochimaru has always been interested in the power of the Uzumaki clan and Naruto's nine - tailed fox power. He could be using Kushina as a tool to get to Naruto.
Maybe the main antagonist is an ancient evil that has awakened. It has the power to manipulate Artemis's mind, making her kidnap Percy against her will. This evil entity wants to use Percy as a sacrifice to gain more power. So, while Artemis is the one who physically kidnaps Percy, the real force behind it, the ancient evil, is the true antagonist.
A powerful and corrupt organization might be the main antagonist. They blackmail Wade into kidnapping Peter. The organization wants to study Peter or use him as a bargaining chip. Wade is caught in a difficult situation where he has to protect Peter from this organization while also dealing with the fact that he has kidnapped him.
The main antagonist could be the head of the CIA operation that orders Link's kidnapping. This person might be power - hungry and believe that Link can be used to gain more control or knowledge.