Perhaps a group of inter - dimensional bounty hunters. They've heard about Loki's children and the potential power they might possess when they grow up. So they target the children to either sell them to the highest bidder or use their powers for their own evil purposes. Tony then has to fight against this group to save the kids.
Another possibility is a rogue Asgardian who has turned against Loki. This Asgardian feels that Loki's children are a threat to the stability of Asgard or the Nine Realms. So they set out to eliminate the children. Tony gets involved when he hears about this plan through some channels and decides to stop this rogue Asgardian.
Well, perhaps Loki's children are being hunted because of their unique powers. Tony stumbles upon their situation. He starts by gathering information about Loki's kids and the threats they face. Then he devises a plan. He might upgrade his suit to deal with the magical elements involved. Along the way, he could form an unexpected bond with the children, teaching them about the modern world while protecting them from harm.
It could be someone who is manipulating Loki to kidnap the Hulk. Maybe an even more powerful villain from the Marvel universe, like Thanos. He might be using Loki as a pawn to get the Hulk for his own evil purposes.
In the fanfiction, Loki may have developed a sense of respect or even friendship for Tony. They are both very intelligent characters. Loki might admire Tony's ingenuity and courage. So when he realizes that Tony is in danger in Siberia, his new - found feelings for Tony drive him to save his life. Also, Loki might be bored with his usual villainous ways and wants to do something good for a change, and saving Tony seems like a good start.
It could be someone from Stark Industries who doesn't like the idea of Peter inheriting something. Maybe a rival within the company who sees Peter as an inexperienced kid and wants to take whatever Tony left for Peter for themselves.
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.
It could be another powerful deity from either the Norse or the Christian pantheon who doesn't want Gabriel and Loki to team up. Maybe a more rigid and traditional angel who thinks Gabriel is consorting with the wrong crowd by interacting with Loki.
Perhaps it's a group of mercenary ninjas. They've been hired by someone who has a grudge against Zabuza. They see Zabuza as an easy target when he's alone or vulnerable, but Naruto shows up to spoil their plan.
It could be Palpatine. Since Anakin is going against his wishes by saving the younglings, Palpatine would see this as a threat to his plans. He might send more clone troopers or even some of his dark side minions to stop Anakin.
Perhaps a new and original antagonist could be created for this fanfiction. This antagonist could be a rogue ninja who has mastered a forbidden jutsu that allows him to manipulate time as well. He could be the one who sets up the events that lead to Minato's endangerment, and Naruto has to figure out his motives and stop him while also saving Minato.
It could be a rogue ninja who is using the poochyena for some sort of evil experiment. Naruto has to stop this ninja from harming the poochyena.