The Vulture could be a new and more menacing villain. Maybe he's using the post - Civil War chaos to his advantage, stealing high - tech equipment that was left unguarded during the Avenger's split. He could be targeting Spider - Man specifically, seeing him as an easy target now that he doesn't have the full support of the Avengers.
There could be a genetic engineer gone bad. This villain creates dangerous hybrid creatures and releases them in the city, forcing Spider - Man 2099 to fight these unpredictable beasts. He might also have to figure out how to reverse the genetic mutations.
His relationships within the superhero community would shift. Some heroes might respect his decision and stand by him, while others might think he's being reckless. This could create rifts and new alliances within the already divided superhero groups during the Civil War in the fanfiction story.
One interesting plotline could be Spider - Man trying to regain the trust of the public. After the events of Civil War, he might be seen as a bit of a wildcard. So, he could be doing small - scale heroics to show that he's still on the side of the good. For example, helping out at local charities or stopping petty crimes in a very public way to win back the hearts of the people.
The Lizard could be turned into a more supernatural villain. Maybe he gets possessed by an ancient spirit that makes him not only stronger but also able to control other reptiles with dark magic. This would pose a huge threat to Spider - Man as he has to deal with the Lizard's new powers on top of his already dangerous physical abilities.
Well, there could be a new mentor figure for the reincarnated Spider Man. Maybe an old - time hero who has been around for centuries and has a lot of wisdom to pass on. This character could help the new Spider Man understand his powers and his purpose in this new life.
Green Goblin is another option. He might take advantage of the divided superhero community. He could target Spider - Man specifically, knowing that with the other heroes at odds, there's less chance of them coming to his aid. He could also try to use the conflict to his advantage in his criminal activities, like stealing from places that are unguarded because the heroes are busy fighting each other.
One idea could be that Peter Parker decides to unmask himself as a political statement during the Civil War. He might feel that the secrecy in the superhero community is causing more harm than good and by unmasking, he hopes to start a new era of transparency among heroes.
In a fanfiction, Spider - Man could also die due to friendly fire. With the heroes split in the Civil War and the chaos of battle, it's possible that a misaimed attack from one of the heroes accidentally hits Spider - Man and causes his death.
One great fanfiction could be about Spider - Man's internal struggle during the events of 'Captain America: Civil War'. He's a new addition to this complex world of superhero politics. He might be initially excited to be part of the fight, but then starts to question the motives of both sides. Maybe he tries to find a middle ground, using his unique perspective as a young hero who hasn't been jaded by years of superhero rivalries.
A shadow - ninja character could be introduced. This character could be an anti - hero at first, with his own motives in the world of shadows, but later teams up with Spider - Man.