A new supervillain who has emerged and wants to make a name for themselves. They think that kidnapping Tony Stark's daughter will draw him out and give them the chance to prove they are a force to be reckoned with. They might also be after Tony's wealth and resources which they can access through his daughter.
Well, the plot could involve Tony Stark using all his high - tech resources to search for his daughter. Maybe she was kidnapped by one of his enemies as a way to get to him. He could team up with the Avengers to scour the globe for her.
It could be some of Tony's business rivals. They might see the daughter as a way to get to Tony, either to steal his technology secrets or to blackmail him. They could try to kidnap her or manipulate her into betraying her father.
In this fanfiction, the plot might involve the daughter inheriting Tony's intelligence and technological skills. She could be a prodigy in her own right, building her own gadgets in secret. When Tony finally discovers her existence, he's both proud and worried. There could be a conflict with other characters who either want to protect the daughter or use her abilities for evil purposes. And as the story progresses, she might join forces with the Avengers or form her own team to fight against the bad guys.
One possible reason could be a miscommunication plot device. Maybe in the fanfiction, the daughter has secrets that Tony misinterprets as betrayal. Another reason might be that the writer wants to explore a more complex and less idealized relationship between them. For example, if the daughter has powers that are uncontrollable and pose a threat, Tony, being the cautious and responsible figure he is, might initially react with hatred out of fear for the safety of others.
One way is to add more backstory to both Tony and his daughter. By exploring their pasts, we can understand better why he might hate her. For example, if there was a past incident that led to a misunderstanding between them. Another way is to introduce a third party that can either make the situation worse or help resolve it. A character like Pepper Potts could try to mediate between them.
Danzo could be a great antagonist. He always had his own secretive and often unethical plans. He might see Naruto as a threat even if he's innocent and frame him as a missing - nin to get rid of him.
It could be a new dark wizard that we haven't seen in the original series. This wizard might be jealous of Harry's fame and power and wants to eliminate him by making him disappear.
Maybe it's an old clock - maker named Mr. Grimsby. He has a dark past related to a cursed clock he once made. When he hears about Tony's interest in clocks, he fears that Tony will discover his secret. So he tries to stop Tony from delving deeper into the world of clocks by causing problems in Tony's life, like getting him fired from his job at the local clock shop.
There could be characters from Tony's past as well. For example, Obadiah Stane might be mentioned or even be a part of some backstory. If the fanfiction delves into the family history, there could be appearances of their parents in flashbacks. And don't forget Rhodey. He could be a great influence on the baby sister, teaching her about military values or just being a cool older friend.
The mother's new partner. He doesn't want the forgotten daughter to be part of the family as he fears she will disrupt the new family dynamic he has been trying to build. He might use various means to keep her away from the family.