A witch who has a grudge against the vampire world might be the main antagonist. She doesn't like the idea of a human - vampire relationship like Damon and Elena's. So when they first meet, she starts to cast spells to cause chaos in their lives. She might make Elena forget parts of their meeting or make Damon see illusions of Elena in danger, which could drive a wedge between them right from the start.
Another possible antagonist could be a powerful vampire hunter. He sees Damon as a threat and Elena as a potential target or a way to get to Damon. When Damon and Elena meet, this hunter is already watching them. He plans to use their new relationship against them, making their first meeting the start of a lot of trouble for both of them.
Well, it could be that they meet in a mysterious forest. Damon might be on one of his brooding walks when he stumbles upon Elena. Maybe she's lost or just enjoying the solitude. Their eyes meet and there's an instant spark of curiosity and something more. They exchange a few words, and Damon's charm starts to work on Elena.
Another group could be the vampire hunters. If they find out about the baby, they would likely see it as an abomination and try to kill it. They could be a constant threat, forcing Damon and Elena to keep moving and hiding. They might also team up with other supernatural enemies of Damon and Elena to try and take down the baby.
It could be a vampire who resents Damon for becoming human. This vampire might see it as a betrayal of their kind. They could try to either turn Damon back into a vampire against his will or simply make his human life miserable.
It could be an old vampire enemy of Damon's. Maybe someone from his past who has a vendetta against him and sees the baby as a way to get revenge. This antagonist could try to kidnap the baby or cause trouble in their lives.
It could be an old vampire who sees Elena as a threat to his power or territory. Maybe he doesn't like the idea of a newly - turned vampire causing a stir in the vampire community and decides to take her out.
Well, perhaps the plot could involve Damon and Elena having an instant connection. Maybe Damon saves Elena from some sort of danger in this fanfic, which starts their relationship on a very different foot compared to the original story. It could also be that they share a deep conversation right away, revealing parts of their personalities that they usually keep hidden.
It could be Dr. Eggman. Maybe he has sent some of his robots to the area where Sonic and Tails first meet. The robots are causing chaos and Sonic and Tails have to team up to stop them, which is how they start to bond.
A powerful witch could be the antagonist. She might have been the one who turned Damon human again against his will, and now she has some sinister plan for him. For example, she wants to use his new human form to perform some dark magic ritual that requires a human with a vampire past.
It could be a powerful sorcerer from the time she travels back to. This sorcerer might sense that Elena doesn't belong in that time and wants to stop her from interfering with his plans. Maybe he has some dark magic he wants to use to take over the kingdom or town she's in.
I think Stefan can be a really liked character in these fanfictions even though he's in a bit of a love triangle situation. His complex relationship with Damon and his past with Elena make him an interesting addition. He might be shown as still caring for Elena but also coming to terms with her love for Damon. Also, Alaric is a character that many fans like. He can act as a mentor or a voice of reason in the fanfiction, and his relationship with Damon and Elena can be explored in different ways.