One idea could be that during a mission crossover, Spider - Man gets injured while trying to protect a civilian from an unexpected attack by a powerful enemy. Maybe he takes a hit meant for an Avenger and his suit's technology malfunctions, leaving him vulnerable.
Perhaps in a darker fanfiction, Spider - Man is injured in an Avengers crossover when he is betrayed by one of the Avengers (under some mind - control or false belief). This Avenger attacks him, and Spider - Man, being caught off - guard, sustains serious injuries. His healing factor might not be enough to quickly recover from such a betrayal - induced wound, and he has to deal with the physical and emotional pain.
He could be injured by a new and powerful villain that the Avengers and Spider - Man are facing together. The villain might have a weapon or power that can penetrate Spider - Man's suit and defenses, like a sonic blast that disrupts his spider - sense and then physically harms him.
The Avengers would be very concerned. Captain America would immediately take charge of the situation, trying to keep everyone calm while they assess Spider - Man's injuries. Iron Man would start scanning for the best way to treat him, using his high - tech equipment. Thor might offer some of his Asgardian knowledge of healing, if there was any. Black Widow and Hawkeye would be on guard, making sure there were no further threats while the team focused on Spider - Man.
One idea could be that Spider - Gwen somehow gets transported to the Avengers' universe. Maybe Doctor Strange's magic goes awry during an experiment. She could team up with Black Widow, sharing her acrobatic skills and they take on a group of villains together. It would be a cool dynamic as Gwen is more of a street - level hero while the Avengers often deal with bigger threats.
In a fanfic, Spider - Man could be injured while on a mission with the Avengers in outer space. Maybe they are exploring an alien planet and are attacked by some sort of bio - mechanical creatures. Spider - Man is separated from the group and gets severely injured by one of the creatures' acidic attacks. His injury makes it difficult for him to use his powers effectively, and the Avengers have to find a way to both get him back to Earth and find a cure for his injury.
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.
In a fanfiction, Spider - Man could get lost in an alternate dimension during a mission. The Avengers then have to find a way to bring him back. While in the alternate dimension, Spider - Man meets different versions of the Avengers and has to fight his way through various challenges to return home.
One plot idea could be that Spider Man gets injured during a fight with a new super - villain. As he's injured, he has to rely on his friends and the citizens of New York to help him hide from the villain's minions while he recovers. Maybe Mary Jane finds him and nurses him back to health in a secret location.
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.
In a Harry Potter and Spider - Man crossover fanfiction, perhaps the Venom symbiote attaches itself to a Hogwarts student. Spider - Man then has to travel to the wizarding world to stop the now - corrupted student from causing chaos. Along the way, he discovers that the magic in the wizarding world can both help and hinder his attempts to subdue the symbiote - controlled student. Harry and his friends might initially be suspicious of Spider - Man but then realize they need his unique skills.
One idea could be that the Avengers are initially shocked but then become very protective of Spider - Man. They might start to train him more carefully, like Tony Stark making sure his suit has extra safety features. Another could be that some of the Avengers, like Captain America, take on a mentor role, teaching him about responsibility and heroism in a more age - appropriate way.