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.
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.
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.
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.
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.
In some fanfictions, the story could start with Spiderman saving a girl from a vampire attack. But then he realizes that the vampire has a strange symbol on its body that is related to a Transformer cult. Spiderman delves deeper into this mystery and discovers that there is a plot to use vampire blood to power a doomsday Transformer device. He has to race against time to stop this from happening. Along the way, he may face many challenges, including other vampires who are loyal to the cause, and some Transformer - like guardians who are protecting the device for their own reasons.
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.
A storyline could involve Nightwing being framed for a crime in Gotham. Batman, believing the evidence at first, tries to bring him in. Nightwing, of course, resists as he is innocent, and this leads to their fight. As the story progresses, they both realize there's a bigger conspiracy at play.
One possible storyline could be that Thanos arrives on Earth seeking a powerful artifact. Superman steps in to stop him. They battle it out across the city, with Superman using his strength and speed to try and take down Thanos. Another could be that Thanos somehow manages to get Superman under his control using the Infinity Stones, and then the rest of the Justice League has to figure out how to free Superman and defeat Thanos.