Well, perhaps Spiderman is poisoned by a new type of toxin from a villain. The Avengers then scramble to find an antidote. Black Widow uses her espionage skills to track down the origin of the toxin, while Hulk, in his Banner form, tries to analyze it scientifically. Thor might also use his Asgardian knowledge to see if there are any magical cures. In the meantime, they keep Spiderman comfortable and safe from further attacks.
One reason could be a false accusation. If Spiderman is wrongly accused of a crime by the Avengers or someone within the Avengers' circle, he might feel betrayed and lash out at them. He's just a young hero, and such a false accusation could really make him angry.
Perhaps there is a powerful artifact that both Spiderman and the Avengers are after. They end up in a conflict over it. Spiderman, with his street - smart ways, tries to outwit the Avengers and get the artifact for himself, believing he can use it for good in his own way.
Perhaps there's a power - stealing device in the fanfiction. It's stolen by a villain and used on the Avengers, but Gwen is immune. So the Avengers, now with reduced powers, end up fighting Gwen who is trying to get the device back. Or it could be that Gwen discovers a threat to her world that the Avengers don't believe in, and they try to stop her from taking action, leading to a conflict.
One possible reason could be that Tony initially misunderstands Spiderman's actions. He might think Spiderman is doing something wrong when in fact he's not, and then later realizes his mistake and tries to make it up by helping him. For example, if Spiderman is involved in a situation where it looks like he's causing destruction, but it's actually part of a bigger plan to stop a greater evil.
There are also storylines where Spiderman's secret identity is at risk within the Avengers. Maybe a villain has found a way to infiltrate the team and is trying to expose him. This creates a lot of tension and drama as Spiderman has to protect his identity while still being part of the team.
One popular storyline might involve Spiderman having to balance his relationships with different Avengers while also dealing with his superhero duties. For example, he could be in a relationship with Black Widow, who helps him understand the darker side of the superhero world, and at the same time be friends - with - benefits with Scarlet Witch, who adds a magical and mysterious element to his life. Another could be where he forms a polyamorous relationship with some of the younger Avengers like Shuri and Kate Bishop, and they all work together to take on new threats in the Marvel universe.
In some fanfiction, Spiderman might hurt the Avengers due to mind control. For example, if a powerful villain like Loki gets hold of Spiderman and forces him to fight against the Avengers, he could cause harm. Another possibility is a misunderstanding. Spiderman might be tricked into believing that the Avengers are a threat and act accordingly.
One possible storyline could be that in a battle against a powerful new villain, Spiderman sacrifices himself to save the other Avengers. He might use his web - slinging skills to hold back a deadly explosion or some sort of dark energy blast that was headed towards his teammates. Another could be that he is poisoned by a new kind of toxin created by an evil scientist working for a bigger bad guy in the Avengers' universe. As he slowly succumbs to the poison, he has some touching moments with the other Avengers, like giving Tony Stark a piece of advice on how to be a better hero, and finally passes away.
Perhaps a fanfiction could explore what would happen if Spiderman was the one to first discover a major flaw in Ultron's plan. Since he's a street - level hero with a different perspective from the more global - minded Avengers, he might see something that they miss. His attempts to convince the Avengers about this flaw could create a lot of drama and action in the story.
One possible storyline could be that Spiderman and Batgirl team up to fight a common enemy. Maybe a new super - villain has emerged in Gotham that has some connection to New York, so they join forces. Their different skills, like Spiderman's web - slinging and Batgirl's martial arts, would make for an interesting dynamic in combat.