If it's a crossover with the Fantastic Four, perhaps a cosmic entity is attacking Earth. Spider Man teams up with them to stop it. But during the battle, he's exposed to some deadly radiation from the entity. Despite the Fantastic Four's efforts to save him, his body can't withstand it, and he dies. His death could lead to the Fantastic Four creating new safety protocols for future battles.
It could be Doctor Doom. He might be seeking to take over multiple universes in a crossover. Spider Man stands in his way, and Doom, with his superior intellect and powerful magic, manages to defeat Spider Man. His death would then be a huge shock to other heroes in the crossover, like the Avengers or the Fantastic Four who then have to avenge him.
Well, if Spider - Man died in a Civil War fanfiction, it could be that his death serves as a catalyst for the end of the war. His death might make both sides realize how pointless their fighting is. Maybe the heroes would then come together to honor his memory and try to make amends. His friends in the superhero community, like Ned if he knew about Peter's identity, would be heartbroken. And villains might take advantage of the situation, thinking the heroes are weakened without Spider - Man, which could lead to new threats emerging in the fanfiction world.
One possible scenario could be that Spider Man sacrifices himself to save the city from a powerful and unstoppable villain. He might use all his strength and powers to defeat the enemy, but in the process, his body gives out due to the extreme exertion.
A Spider Man and Nebula fanfiction could be really interesting. Maybe it could be about Spider Man getting accidentally transported to the Guardians of the Galaxy's universe and teaming up with Nebula. They could use their unique skills to fight a common enemy, like a powerful alien warlord who wants to destroy both their home planets.
There could be a situation where a Transformer's technology gets mixed with Oscorp's experiments. This creates a new kind of threat that Spider - Man has to face. The Transformers get involved because it's their technology that's been misused. Together, they figure out a way to reverse the effects and defeat the new hybrid - like villains.
He could become more withdrawn. Losing Aunt May, who was like a mother to him, would be a huge blow. He might isolate himself from his friends and even from his crime - fighting duties for a while as he deals with his grief.
One idea could be a crossover with the X - Men. Spider - Man could team up with Wolverine. Their different fighting styles would make for some amazing action scenes. Wolverine's brute strength and healing factor combined with Spider - Man's agility and web - slinging abilities would be a great combination.
A crossover with Captain America could be great too. Spider - Man, with his youth and modern - day sensibilities, could learn a lot from Cap's old - fashioned values. They could fight side by side against Hydra agents or other villains, and Spider - Man could show Cap some new tricks when it comes to acrobatics in combat.
Captain America could also be an interesting crossover. They have different outlooks - Spider - Man is young and still learning, while Captain America has strong moral values. A story where they team up to stop a group of super - villains who are trying to undermine the city. Captain America could teach Spider - Man about leadership and making tough decisions.