Voldemort's remaining followers could be the antagonists. Even though Voldemort is gone, there are still some Death Eaters who are bitter about their loss. They might see Harry leaving with Fleur as an opportunity to get revenge on Harry or to use Fleur as a hostage to gain power. They could try to ambush them on their journey, creating a lot of dangerous situations for Harry and Fleur.
It could be that they leave to attend a special magical training that is only available in a very secluded place. They might have received an invitation from a very powerful and reclusive wizard. This training could enhance their magical abilities in ways that Hogwarts or Beauxbatons couldn't. They see this as an opportunity to become stronger and more self - reliant, so they leave together, excited for the new challenges and knowledge that awaits them.
In some fanfictions, Fleur might leave Bill for Harry because she realizes that Harry has a certain selfless quality that she admires more. Harry's constant fight against evil and his willingness to sacrifice himself could be very appealing to Fleur. Also, it could be that the fanfiction is set in a situation where Bill is involved in something that Fleur morally opposes, and Harry represents a more morally upright choice for her.
Maybe it's a group within the Ministry of Magic who oppose Harry's influence on Teddy. They might see Harry as trying to groom Teddy to be his successor in some way and want to stop them from leaving together to prevent this.
Voldemort could still be the main antagonist. Even if Harry leaves his parents early, Voldemort might be hunting for him due to the prophecy. His dark presence would be a constant threat, driving Harry's actions and the plot of the fanfiction.
Maybe Voldemort. If the fanfiction combines the Twilight and Harry Potter universes, Voldemort might see Edward as a threat because he is a vampire and could be allied with Harry. So he tries to drive a wedge between them and make Edward leave Harry.
Voldemort could be the antagonist. He might find out that Harry needs Fleur to live and try to capture or kill Fleur to get at Harry. Since Harry is a threat to his power, eliminating the person Harry depends on for his life would be a strategic move for Voldemort.
It could cause a great deal of shock and gossip. The Weasley family, especially Bill's siblings, would likely be very angry and confused. There might be a rift between the Weasleys and Fleur, and perhaps even some tension between the Weasleys and Harry. After all, Bill is a well - liked member of the wizarding community.
It could be a rogue dark wizard who has a personal grudge against Fleur. He might see Harry as an obstacle in his path to harm Fleur. So he captures Harry and tortures him, thinking that it will stop Harry from interfering with his evil intentions towards Fleur.
Often, Luna Lovegood can be found in such fanfictions. Her unique and dreamy nature could bring a different dynamic to the harem. Neville Longbottom might also be involved in some way, perhaps as a friend who supports the harem and helps them out in times of need. There could also be some foreign exchange students or magical creatures in human form that end up in the harem for various reasons.
There could be. Fanfiction is a vast world. Some authors might explore such a complex relationship shift in their stories. However, it might not be as common as more typical pairings in the Harry Potter fandom. You could also check fanfiction communities on Reddit or Tumblr for recommendations.