Another possibility is that the antagonists are a part of a secret organization. They might be operating in Siberia for some hidden purpose and see Tony as a threat or a valuable asset. Their actions against Tony could be part of a larger, more complex plan, and Natasha has to figure out their motives and stop them while rescuing Tony.
There might be a new villain or a previously known enemy who has set a trap for Tony in Siberia. This antagonist could be a powerful figure with their own motives, like wanting to take over Stark Industries or gain access to Tony's Iron Man suits. Natasha would then have to face this antagonist to save Tony. They could have their own army or special powers that make the rescue mission more difficult for Natasha.
Well, without having read the 'peter saves tony from siberia fanfiction', I can only guess. It could start with Peter finding out that Tony is in trouble in Siberia. He then embarks on a journey there. Once he arrives, he might face challenges like harsh weather conditions in Siberia and also potential threats from enemies. Peter would likely use his wits and powers to get to Tony and save him. For example, he could swing through the icy landscapes or use his strength to break through barriers to reach Tony.
There could be a local Siberian healer who becomes an important figure in Tony's life, helping him with his pregnancy.
Peter might become more confident in his abilities. Saving Tony from Siberia is no easy feat, and successfully doing so could boost his self - assurance as a hero.
It could be some dark magic users from Lucy's world who see her as a threat. They might be trying to stop her from using her magic for good.
Maybe some of Tony's business rivals who have access to advanced technology. They could be jealous of Tony's relationship with Ultron and try to harm him. They might hire mercenaries or develop their own weapons to go after Tony. In this fanfiction, these rivals would be the main antagonists as they constantly try to break through Ultron's protection of Tony.
It could be a new villain that we haven't seen in the original Marvel universe. This villain might be able to manipulate Natasha's emotions and loyalty, making her betray Tony. For example, a powerful sorcerer who uses dark magic to control her.
Maybe an old enemy from their time on Earth who somehow managed to get into heaven. This enemy could hold a grudge against both of them and wants to take revenge. They might use their knowledge of Tony and Natasha's past weaknesses to try and defeat them in heaven, where the rules are different from Earth.
Sometimes, an old enemy of Nightwing might resurface and take on the Justice League as a way to get to him. For example, a crime lord from Nightwing's past who has amassed new and dangerous technology and uses it to take down the League, thinking that Nightwing will come running to save them.
It could be Team Rocket. They are always causing trouble for Ash, and it would make sense for them to be the ones behind Ash's predicament in this fanfiction. They might have a new evil plan to capture Ash and Sceptile comes to the rescue.
In some fanfictions, an ancient evil entity that has been awakened might be the main antagonist. This entity could be after Ginny because she has some special power or connection that the entity wants to use for its own dark purposes. And of course, there could be a jealous wizard who wants to get rid of Ginny to have Harry all to himself.