One idea could be that the man who disappeared actually time - traveled. He might return with knowledge of future events that could either save or endanger the world in the story's setting.
One idea could be to explore his origin story in more depth. Maybe he has a hidden family or a past trauma that shaped him into the man of iron. Another could be to put him in a different time period, like the future where technology has advanced even more and he has to adapt.
Perhaps in a fanfiction, the Raft is under a siege by an unknown force. Spider - Man, despite being a prisoner, decides to help defend it. He teams up with some of the more morally ambiguous inmates. Together, they have to overcome their differences and fight off the attackers while also dealing with the internal power struggles and security issues within the Raft.
In some Iron Man harem fanfiction, it could be that Tony Stark is transported to an alternate dimension where the rules of relationships are different. There, he finds himself surrounded by female characters who are all vying for his attention. The story could explore how he navigates this new world and these new relationships while still trying to be the hero he is.
One idea could be exploring the relationship between Spider - Man 2099 and other superheroes in the future. Maybe he teams up with a new group of heroes to fight a powerful villain who threatens the entire city.
One plot idea could be Spider Man having to face a powerful new villain all by himself in a post - apocalyptic New York. The city is in ruins, and he has no backup from the Avengers or other heroes. He has to rely on his wits and his web - slinging skills more than ever.
Well, a cool plot could be that there's a scientific experiment gone wrong that fuses Venom and Spider - Man's powers in an unexpected way. They have to figure out how to control these new combined abilities while also dealing with villains who want to steal their power source. Or perhaps Venom gets amnesia and Spider - Man has to convince him that they were once enemies but now need to work together. There could also be a story where Venom's offspring has a different relationship with Spider - Man, like it's more of an anti - hero sidekick.
One idea could be Spider Man having to team up with his greatest villains to fight a common enemy from another dimension. This would force him to put aside his differences and find a way to work with the likes of Green Goblin and Doctor Octopus.
One idea could be that Spider - Man discovers a new villain who has a personal vendetta against him for something he unknowingly did in the past. This villain targets the people Spider - Man cares about, like Aunt May or Mary Jane, forcing him to go on a full - throttle revenge mission to protect them and clear his name.
A cool plot could involve Spider - Man trying to protect a famous Vegas performer who has a secret that a group of villains wants to expose. This would lead to some epic battles across the Vegas strip.
Well, a plot idea could be that in the fanfiction, the events of Iron Man 3 somehow get re - written in a way that Tony Stark's suits in that movie have a different origin. For example, they were actually created by an ancient civilization that he discovers accidentally, and this new knowledge ties into the Avengers' overall story arc. Also, we could have a story where the Extremis virus from Iron Man 3 spreads in a different way and starts to affect some of the other Avengers. This would force Iron Man to not only deal with his own problems related to the virus but also find a cure for his teammates. And then there's the idea of a parallel universe where Iron Man 3 never happened as we know it, but the Avengers are still dealing with the consequences of a similar threat, and they have to rely on Iron Man's knowledge from that 'alternate' Iron Man 3.