One reason could be his own clumsiness. Maybe Peter is always in a rush and not paying enough attention to his surroundings. For example, he could be running down the stairs while looking at his phone and trip, resulting in an injury.
Peter might get injured while trying to help someone else. He could be so focused on saving a friend from a dangerous situation, like a collapsing building, that he forgets about his own safety and gets hit by falling debris.
It could be due to the actions of a villain. In a fanfiction set in a superhero - like world, a villain might target Peter. The villain could use some sort of weapon or power that harms Peter, like shooting a beam of energy at him which causes burns or bruises.
John could get injured due to the actions of a villain. The villain might set a trap for him. For instance, the villain could rig a staircase to collapse when John steps on it. This would cause John to fall and get injured, perhaps with broken bones or internal bleeding, as part of the villain's evil plan to stop John from achieving his goals.
One reason could be her inexperience in combat. Despite her growth, she is still not as skilled as some of her companions. For example, when facing a new type of demon she might misjudge its attack pattern and get injured. Another reason could be her curiosity. If she wanders off alone into an unknown area, she could easily step into a trap or encounter a hidden danger, like a poisonous plant or a concealed pitfall.
He could be exploring an old, abandoned building and fall through a rotten floorboard.
Another reason could be an accident. In some fanfictions, the setting might be more of a daily - life scenario with a twist. Perhaps Usagi is distracted while walking and trips over something, resulting in an injury. This can add a touch of realism to the otherwise fantastical world she lives in.
Peter was playing football with his team. In a fierce tackle, he was pushed too hard and his ankle twisted in an unnatural way. The pain was immediate and intense. His teammates stopped the game and gathered around him. One of them, who had some first - aid knowledge, tried to immobilize his ankle. Then they carried him to the side of the field and called for his parents to come pick him up and take him to the doctor.
Well, one reason could be that he's on a secret mission for S.H.I.E.L.D. that requires him to go undercover and cut off all contact. Maybe he's investigating a new super - villain threat that's too dangerous to let anyone know about.
It could also be due to external pressure. The media or some powerful figures in the fanfiction world might force Tony to stay away from Peter. They could spread false rumors about their relationship or use their influence to separate them for their own gain.
In fanfiction, she could be injured during a battle against dark wizards. Maybe she was caught off - guard while trying to protect her friends.
Maybe it's due to a new and powerful enemy's attack. In fanfiction, authors might create unique villains with abilities that specifically target Peter's weaknesses. For example, if the villain has the power to disrupt Spider - Man's enhanced senses, it could cause Peter to be disoriented and ultimately collapse. Another aspect could be that Peter overuses his powers without proper rest, which exhausts his body and causes him to collapse.
In the fanfiction, Maryjane could be in love with someone else at the time. Even if she has some feelings for Peter, her stronger feelings for another person make her reject Peter. Also, Peter might have done something in the past that Maryjane can't forgive, like lying to her, which results in the rejection.